bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass Transfer of Proteins in Aqueous Two-Phase Systems
Authors: Kaplanow I. , Goerzgen F. , Merz J. , Schembecker G. 
Published: March 2019

AbstractAqueous Two-Phase Extraction is known to be a gentle separation technique for biochemical molecules where product partitioning is fast. However, the reason for the high mass transfer rates has not been investigated, yet. Many researchers claim that the low interfacial tension facilitates the formation of very small droplets and with it a large interfacial area causing a fast partitioning. However, an experimental evidence for this hypothesis has not been published yet. In this study, the mass transfer coefficients of two proteins, namely lysozyme and bromelain, were determined by providing a defined interfacial area for partitioning. Compared to low molecular weight solutes the mass transfer coefficient for the proteins investigated was small proving for the first time that the large interfacial area and not fast diffusion seems to be the reason for fast protein partitioning.
Age-related gene and miRNA expression changes in airways of healthy individuals
Authors: Ong J. , Woldhuis R. R. , Boudewijn I. M. , van den Berg A. , Kluiver J. , Kok K. , Terpstra M. M. , Guryev V. , de Vries M. , Vermeulen C. J. , Timens W. , van den Berge M. , Brandsma C. A. 
Published: March 2019

AbstractKnowledge on age-related miRNA changes in healthy individuals and their interaction with mRNAs is lacking. We studied age-related mRNA and miRNA expression changes and their interactions in normal airways. RNA and small RNA sequencing was performed on bronchial biopsies of 86 healthy individuals (age: 18–73) to determine age-related expression changes. Per age-related miRNA we determined the enrichment of age-related predicted targets and their correlation. We identified 285 age-related genes and 27 age-related miRNAs. Pathway enrichment showed that genes higher expressed with age were involved in synapse-related processes. Genes lower expressed with age were involved in cell cycle regulation, the immune system and DNA damage/repair. MiR-146a-5p, miR-146b-5p and miR-142-5p were lower expressed with increasing age and we found a significant enrichment for predicted targets of these miRNAs among genes that were higher expressed with age. The expression levels of the enriched predicted targets RIMS2 and IGSF1 were negatively correlated with both miR-146a-5p and miR-146b-5p. RIMS2 was present in the enriched process, i.e. positive regulation of synaptic transmission. In conclusion, genes decreased with ageing are involved in several of the ageing hallmarks. Genes higher expressed with ageing were involved in synapse-related processes, of which RIMS2 is potentially regulated by two age-related miRNAs.
Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae
Authors: Wang Chunlian , Tariq Rezwan , Ji Zhiyuan , Wei Zheng , Zheng Kaili , Mishra Rukmini , Zhao Kaijun 
Published: March 2019

AbstractBacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease in most of the rice growing regions worldwide. Among the 42 BB resistance (R) genes, Xa23 is an executor R gene, conferring broad-spectrum disease resistance to all naturally occurring biotypes of Xoo. In this study, CBB23, a rice line carrying Xa23 gene, was inoculated with wild PXO99A and its mutant, P99M2, to retrieve the differentially expressed genes (DEGs). RNA-Seq analysis retrieved 1,235 DEGs (p-value ≤ 0.05) at 12, 24, 36, and 48 hours of post inoculation (hpi). Gene ontology (GO) analysis classified the DEGs functionally into biological process, cellular component and molecular function. KEGG pathway analysis categorized the DEGs into 11 different pathways, and the ribosome is a prominent pathway followed by biosynthesis of phenylpropanoids. Gene co-expression network analysis identified the clusters of transcription factors (TFs) which may be involved in PXO99A resistance. Additionally, we retrieved 67 differentially expressed TFs and 26 peroxidase responsive genes which may be involved in disease resistance mechanism. DEGs involved in the host-pathogen interaction, e.g., signaling mechanism, cell wall and plant hormones were identified. This data would be a valuable resource for researchers to identify the candidate genes associated with Xoo resistance.
Reconstructing Taiwan’s land cover changes between 1904 and 2015 from historical maps and satellite images
Authors: Chen Yi-Ying , Huang Wei , Wang Wei-Hong , Juang Jehn-Yih , Hong Jing-Shan , Kato Tomomichi , Luyssaert Sebastiaan 
Published: March 2019

AbstractA new reconstruction of changes in Taiwan’s land cover and estimated uncertainty between 1904 and 2015 is presented. The reconstruction is made by integrating geographical information from historical maps and SPOT satellite images, to obtain spatially explicit land cover maps with a resolution of 500 × 500 m and distinguishes six land cover classes: forests, grasslands, agricultural land, inland water, built-up land, and bare soil. The temporal resolution is unbalanced being derived from four historical maps describing the land cover between 1904 and 1994 and five mosaic satellite images describing the land cover between 1995 and 2015. The uncertainty of the historical maps is quantified to show the aggregation error whereas the uncertainty of the satellite images is quantified as classification error. Since 1904, Taiwan, as a developing country, has gone through a not unusual sequence of population growth and subsequent urbanization, a decoupling of the demand for agricultural land from population growth, and a transition from shrinking in forest area to forest expansion. This new land cover reconstruction is expected to contribute to future revisions of global land cover reconstructions as well as to studies of (gross) land cover changes, the carbon budget, regional climate, urban heat islands, and air and water pollution at the national and sub-national level.
Vector uncoating limits adeno-associated viral vector-mediated transduction of human dendritic cells and vector immunogenicity
Authors: Rossi Axel , Dupaty Léa , Aillot Ludovic , Zhang Liang , Gallien Célia , Hallek Michael , Odenthal Margarete , Adriouch Sahil , Salvetti Anna , Büning Hildegard 
Published: March 2019

AbstractAAV vectors poorly transduce Dendritic cells (DC), a feature invoked to explain AAV’s low immunogenicity. However, the reason for this non-permissiveness remained elusive. Here, we performed an in-depth analysis using human monocyte-derived immature DC (iDC) as model. iDC internalized AAV vectors of various serotypes, but even the most efficient serotype failed to transduce iDC above background. Since AAV vectors reached the cell nucleus, we hypothesized that AAV’s intracellular processing occurs suboptimal. On this basis, we screened an AAV peptide display library for capsid variants more suitable for DC transduction and identified the I/VSS family which transduced DC with efficiencies of up to 38%. This property correlated with an improved vector uncoating. To determine the consequence of this novel feature for AAV’s in vivo performance, we engineered one of the lead candidates to express a cytoplasmic form of ovalbumin, a highly immunogenic model antigen, and assayed transduction efficiency as well as immunogenicity. The capsid variant clearly outperformed the parental serotype in muscle transduction and in inducing antigen-specific humoral and T cell responses as well as anti-capsid CD8+ T cells. Hence, vector uncoating represents a major barrier hampering AAV vector-mediated transduction of DC and impacts on its use as vaccine platform.
Selective oxidation of B800 bacteriochlorophyll a in photosynthetic light-harvesting protein LH2
Authors: Saga Yoshitaka , Kawano Kiyoshiro , Otsuka Yuji , Imanishi Michie , Kimura Yukihiro , Matsui Sayaka , Asakawa Hitoshi 
Published: March 2019

AbstractEngineering chlorophyll (Chl) pigments that are bound to photosynthetic light-harvesting proteins is one promising strategy to regulate spectral coverage for photon capture and to improve the photosynthetic efficiency of these proteins. Conversion from the bacteriochlorophyll (BChl) skeleton (7,8,17,18-tetrahydroporphyrin) to the Chl skeleton (17,18-dihydroporphyrin) produces the most drastic change of the spectral range of absorption by light-harvesting proteins. We demonstrated in situ selective oxidation of B800 BChl a in light-harvesting protein LH2 from a purple bacterium Rhodoblastus acidophilus by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. The newly formed pigment, 3-acetyl Chl a, interacted with the LH2 polypeptides in the same manner as native B800. B850 BChl a was not oxidized in this reaction. CD spectroscopy indicated that the B850 orientation and the content of the α-helices were unchanged by the B800 oxidation. The nonameric circular arrangement of the oxidized LH2 protein was visualized by AFM; its diameter was almost the same as that of native LH2. The in situ oxidation of B800 BChl a in LH2 protein with no structural change will be useful not only for manipulation of the photofunctional properties of photosynthetic pigment-protein complexes but also for understanding the substitution of BChl to Chl pigments in the evolution from bacterial to oxygenic photosynthesis.
Amelogenic transcriptome profiling in ameloblast-like cells derived from adult gingival epithelial cells
Authors: Hyun Sun-Yi , Mun Seyoung , Kang Kyung-Jung , Lim Jong-Chan , Kim Shin-Young , Han Kyudong , Jang Young-Joo 
Published: March 2019

AbstractDental enamel is the highly mineralized tissue covering the tooth surface and is formed by ameloblasts. Ameloblasts have been known to be impossible to detect in adult tooth because they are shed by apoptosis during enamel maturation and tooth eruption. Owing to these, little was known about appropriate cell surface markers to isolate ameloblast-like cells in tissues. To overcome these problems, epithelial cells were selectively cultivated from the gingival tissues and used as a stem cell source for ameloblastic differentiation. When gingival epithelial cells were treated with a specified concentration of BMP2, BMP4, and TGFβ-1, the expression of ameloblast-specific markers was increased, and both the MAPK and Smad signaling pathways were activated. Gingival epithelial cells differentiated into ameloblast-like cells through epithelial-mesenchymal transition. By RNA-Seq analysis, we reported 20 ameloblast-specific genes associated with cell surface, cell adhesion, and extracellular matrix function. These cell surface markers might be useful for the detection and isolation of ameloblast-like cells from dental tissues.
Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay
Authors: Saludes V. , Antuori A. , Reinhardt B. , Viciana I. , Clavijo E. , Schreiber L. , Tenenbaum M. , Rodriguez-Frias F. , Quer J. , Matas L. , Martró E. 
Published: March 2019

AbstractAccurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5’NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with “not detected” results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. “Not detected” results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
Circatidal gene expression in the mangrove cricket Apteronemobius asahinai
Authors: Satoh Aya , Terai Yohey 
Published: March 2019

AbstractThe mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors. It shows circatidal rhythmicity, with a 12.6-h period of locomotor activity under constant conditions. Its free-running activity also has a circadian component; i.e. it is more active during the subjective night than during the day. In this study, we investigated rhythmic gene expression under constant darkness by RNA sequencing to identify genes controlled by the biological clock. Samples collected every 3 h for 48 h were analysed (one cricket per time-point). We identified 284 significant circatidal cycling transcripts (period length 12–15 h). Almost half of them were annotated with known genes in the NCBI nr database, including enzymes related to metabolic processes and molecular chaperones. There were less transcripts with circadian rhythmicity than with circatidal rhythmicity, and the expression of core circadian clock genes did not show significant rhythmicity. This may reflect the nature of the mangrove cricket or may be due to the paucity of the sampling repeats: only two periods for circadian cycle with no replications. We evaluated for the first time the rhythmic transcriptome of an insect that shows circatidal rhythmic activity; our findings will contribute to future studies of circatidal clock genes.
Diagnosing Zika virus infection against a background of other flaviviruses: Studies in high resolution serological analysis
Authors: Hansen Sören , Hotop Sven-Kevin , Faye Oumar , Ndiaye Oumar , Böhlken-Fascher Susanne , Pessôa Rodrigo , Hufert Frank , Stahl-Hennig Christiane , Frank Ronald , Czerny Claus-Peter , Schmidt-Chanasit Jonas , Sanabani Sabri S. , Sall Amadou A. , Niedrig Matthias , Brönstrup Mark , Fritz Hans-Joachim , Abd El Wahed Ahmed 
Published: March 2019

AbstractZika virus (ZIKV) is a mosquito-borne flavivirus. Homologous proteins of different flaviviruses display high degrees of sequence identity, especially within subgroups. This leads to extensive immunological cross-reactivity and corresponding problems for developing a ZIKV-specific serological assay. In this study, peptide microarrays were employed to identify individual ZIKV antibody targets with promise in differential diagnosis. A total of 1643 overlapping oligopeptides were synthesized and printed onto glass slides. Together, they encompass the full amino acid sequences of ZIKV proteomes of African, Brazilian, USA, and French Polynesian origins. The resulting ZIKV scanning microarray chips were used to screen three pools of sera from recent Zika outbreaks in Senegal and Cape Verde, in Brazil, and from overseas travelers returning to the EU. Together with a mixed pool of well characterized, archived sera of patients suffering from infections by dengue, yellow fever, tick-borne encephalitis, and West Nile viruses, a total of 42 sera went into the study. Sixty-eight antibody target regions were identified. Most of which were hitherto unknown. Alignments and sequence comparisons revealed 13 of which could be classified as bona fide ZIKV-specific. These identified antibody target regions constitute a founding set of analytical tools for serological discrimination of ZIKV from other flaviviruses.
Engraftment and proliferation potential of embryonic lung tissue cells in irradiated mice with emphysema
Authors: Shiraishi Kazushige , Shichino Shigeyuki , Tsukui Tatsuya , Hashimoto Shinichi , Ueha Satoshi , Matsushima Kouji 
Published: March 2019

AbstractRecently, there has been increasing interest in stem cell transplantation therapy, to treat chronic respiratory diseases, using lung epithelial cells or alveolospheres derived from endogenous lung progenitor cells. However, optimal transplantation strategy of these cells has not been addressed. To gain insight into the optimization of stem cell transplantation therapy, we investigated whether lung cell engraftment potential differ among different developmental stages. After preconditioning with irradiation and elastase to induce lung damage, we infused embryonic day 15.5 (E15.5) CAG-EGFP whole lung cells, and confirmed the engraftment of epithelial cells, endothelial cells, and mesenchymal cells. The number of EGFP-positive epithelial cells increased from day 7 to 28 after infusion. Among epithelial cells derived from E13.5, E15.5, E18.5, P7, P14, and P56 mice, E15.5 cells demonstrated the most efficient engraftment. In vitro, E15.5 epithelial cells showed high proliferation potential. Transcriptome analyses of sorted epithelial cells from E13.5, E15.5, E18.5, P14, and P56 mice revealed that cell cycle and cell-cell adhesion genes were highly enriched in E15.5 epithelial cells. Our findings suggest that cell therapy for lung diseases might be most effective when epithelial cells with transcriptional traits similar to those of E15.5 epithelial cells are used.
Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1)
Authors: Shimizu Chikako , Wakita Yoshihisa , Inoue Takashi , Hiramitsu Masanori , Okada Miki , Mitani Yutaka , Segawa Shuichi , Tsuchiya Youichi , Nabeshima Toshitaka 
Published: March 2019

AbstractPolyphenols have been examined for their beneficial effects on health, particularly in rodents, but their lifelong effects are unclear. Lemons (Citrus limon), containing lemon polyphenols (LPP), are widely consumed but the effects of LPP on aging are unknown. Therefore, we examined the effects of LPP on aging such as aging-related scores, locomotor activity, cognitive functions, and intestinal microbiome using senescence-accelerated mouse prone 1 (SAMP1) and senescence-accelerated resistant mouse 1 (SAMR1). All mice had ad libitum access to water (P1_water group, SAMR1) or 0.1% LPP (P1_LPP group). In the P1_LPP group, LPP intake prolonged the lifespan by approximately 3 weeks and delayed increases in aging-related scores (e.g., periophthalmic lesions) and locomotor atrophy. The P1_water group showed large changes in the intestinal microbiome structure, while the R1 and P1_LPP groups did not. The phylum Bacteroidetes/Firmicutes, which is associated with obesity, in the P1_water group was significantly lower and higher than that in the P1_LPP and R1 groups, respectively. Although the relative abundance of Lactobacillus significantly increased in both P1 groups with aging, the P1_LPP group showed a significantly lower increase than the P1_water group. Thus, lifelong intake of LPP may have anti-aging effects on both phenotypes and the intestinal environment.
Poly-L-Lysine functionalised MWCNT-rGO nanosheets based 3-d hybrid structure for femtomolar level cholesterol detection using cantilever based sensing platform
Authors: Basu Aviru Kumar , Sah Amar Nath , Pradhan Asima , Bhattacharya Shantanu 
Published: March 2019

AbstractIn this work we have developed a novel rGO-MWCNT (reduced graphene oxide-multiwalled carbon nanotube) nanocomposite material with Poly-L-Lysine functionalization which can be used for detection of biomolecules with enhanced sensitivity. The reduced GO sheets are found to play a major role as a connector and helps in the assembly of bundles of carbon nanotubes (CNTs) which may sometime play a role of upstanding nanostructures. The overall composite structure is further fully functionalized resulting in an overall high density of amino groups that can be used to capture biomolecules. The sensitivity of the as synthesized film is tested by the oxidation of cholesterol through cholesterol oxidase enzyme that is biochemically immobilized over these composite films. The test for the immobilization density of the novel films are carried out by mounting these films on sensitive thin section static micro/nano-cantilever platforms. The platforms have capability to measure cholesterol traces in blood upto an extent of 100 femto molar through deflection /bending of the cantilevers due to surface reaction. The films developed show a promise of high immobilization density which is further confirmed through fluorescence studies using FITC labeling of functionalized MWCNT-PLL and rGO-PLL films respectively.
Hybrid approach to sieve out natural compounds against dual targets in Alzheimer’s Disease
Authors: Das Sucharita , Chakraborty Sandipan , Basu Soumalee 
Published: March 2019

AbstractExcess Aβ production by the key protease BACE1, results in Aβ aggregation, forming amyloid plaques, all of which contribute to the pathogenesis of Alzheimer’s disease. Besides the multi-factorial nature of the disease, the diversity in the size and shape of known ligands that bind to the active site of BACE1, that is the flexibility of the enzyme, pose a serious challenge for the identification of drug candidates. To address the issue of receptor flexibility we have carried out ensemble docking with multiple receptor conformations. Therein, two representative structures each from closed and semi-open BACE1 conformations were selected for virtual screening to identify compounds that bind to the active site of both the conformations. These outperformed compounds were ranked using pharmacophore models generated by a ligand-based approach, for the identification of BACE1 inhibitors. The inhibitors were further predicted for anti-amyloidogenic activity using a QSAR model already established by our group thus enlisting compounds with dual potency. BACE1 inhibitory and anti-amyloidogenic activity for the commercially available compounds were validated using in vitro studies. Thus, incorporation of receptor flexibility in BACE1 through ensemble docking in conjunction with structure and ligand-based approach for screening might act as an effective protocol for obtaining promising scaffolds against AD.
A fine-grained time course investigation of brain dynamics during conflict monitoring
Authors: Ruggeri Paolo , Meziane Hadj Boumediene , Koenig Thomas , Brandner Catherine 
Published: March 2019

AbstractThe conflict monitoring model predicting higher anterior cingulate cortex (ACC) neuronal activity on incongruent trials has been recently challenged by a model predicting longer neuronal activity in incongruent trials characterized by longer RTs. To clarify this issue, brain dynamics were explored through event-related-potential (ERP) recordings during a Stroop task. We assessed differences between experimental conditions by combining complementary methods sensitive to the temporality of events including microstate, TANOVA and source localization analysis. The analysis demonstrated the same electrical dynamics only differed in duration towards the end of information processing in the incongruent condition. Specifically, the activation strength of the ACC region did not differ significantly between congruent and incongruent conditions but lasted longer in the incongruent condition. Taken together, our results support the model predicting longer neuronal activity in incongruent trials characterized by longer RTs. They highlight that brain dynamics can dramatically change through periods of interest and that caution is required when interpreting fMRI results. To conclude, these results indicate how time-sensitive measures can contribute to a better understanding of the mechanisms underlying information processing, and thus offer new venues to explore conflict monitoring