bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring and Mapping of Rice Cropping Pattern in Flooding Area in the Vietnamese Mekong Delta Using Sentinel-1A Data: A Case of An Giang Province
Authors: Minh Huynh Vuong Thu , Avtar Ram , Mohan Geetha , Misra Prakhar , Kurasaki Masaaki
Published: May 2019

Cropping intensity is one of the most important decisions made independently by farmers in Vietnam. It is a crucial variable of various economic and process-based models. Rice is grown under irrigated triple- and double-rice cropping systems and a rainfed single-rice cropping system in the Vietnamese Mekong Delta (VMD). These rice cropping systems are adopted according to the geographical location and water infrastructure. However, little work has been done to map triple-cropping of rice using Sentinel-1 along with the effects of water infrastructure on the rice cropping intensity decision. This study is focused on monitoring rice cropping patterns in the An Giang province of the VMD from March 2017 to March 2018. The fieldwork was carried out on the dates close to the Sentinel-1A acquisition. The results of dual-polarized (VV and VH) Sentinel-1A data show a strong correlation with the spatial patterns of various rice growth stages and their association with the water infrastructure. The VH backscatter (σ°) is strongly correlated with the three rice growth stages, especially the reproductive stage when the backscatter is less affected by soil moisture and water in the rice fields. In all three cropping patterns, σ°VV and σ°VH show the highest value in the maturity stage, often appearing 10 to 12 days before the harvesting of the rice. A rice cropping pattern map was generated using the Support Vector Machine (SVM) classification of Sentinel-1A data. The overall accuracy of the classification was 80.7% with a 0.78 Kappa coefficient. Therefore, Sentinel-1A can be used to understand rice phenological changes as well as rice cropping systems using radar backscattering.
Bicycle Level of Service for Route Choice—A GIS Evaluation of Four Existing Indicators with Empirical Data
Authors: Pritchard Ray , Frøyen Yngve , Snizek Bernhard
Published: May 2019

Bicycle Level of Service (BLOS) indicators are used to provide objective ratings of the bicycle suitability (or quality) of links or intersections in transport networks. This article uses empirical bicycle route choice data from 467 university students in Trondheim, Norway to test the applicability of BLOS rating schemes for the estimation of whole-journey route choice. The methods evaluated share a common trait of being applicable for mixed traffic urban environments: Bicycle Compatibility Index (BCI), Bicycle Stress Level (BSL), Sixth Edition Highway Capacity Manual (HCM6), and Level of Traffic Stress (LTS). Routes are generated based on BLOS-weighted networks and the suitability of these routes is determined by finding the percentage overlap with empirical route choices. The results show that BCI provides the best match with empirical route data in all five origin–destination pairs, followed by HCM6. BSL and LTS which are not empirically founded have a lower match rate, although the differences between the four methods are relatively small. By iterating the detour rate that cyclists are assumed to be willing to make, it is found that the best match with modelled BLOS routes is achieved between 15 and 21% additional length. This falls within the range suggested by existing empirical research on willingness to deviate from the shortest path, however, it is uncertain whether the method will deliver the comparable findings in other cycling environments.
NS-DBSCAN: A Density-Based Clustering Algorithm in Network Space
Authors: Wang Tianfu , Ren Chang , Luo Yun , Tian Jing
Published: May 2019

Spatial clustering analysis is an important spatial data mining technique. It divides objects into clusters according to their similarities in both location and attribute aspects. It plays an essential role in density distribution identification, hot-spot detection, and trend discovery. Spatial clustering algorithms in the Euclidean space are relatively mature, while those in the network space are less well researched. This study aimed to present a well-known clustering algorithm, named density-based spatial clustering of applications with noise (DBSCAN), to network space and proposed a new clustering algorithm named network space DBSCAN (NS-DBSCAN). Basically, the NS-DBSCAN algorithm used a strategy similar to the DBSCAN algorithm. Furthermore, it provided a new technique for visualizing the density distribution and indicating the intrinsic clustering structure. Tested by the points of interest (POI) in Hanyang district, Wuhan, China, the NS-DBSCAN algorithm was able to accurately detect the high-density regions. The NS-DBSCAN algorithm was compared with the classical hierarchical clustering algorithm and the recently proposed density-based clustering algorithm with network-constraint Delaunay triangulation (NC_DT) in terms of their effectiveness. The hierarchical clustering algorithm was effective only when the cluster number was well specified, otherwise it might separate a natural cluster into several parts. The NC_DT method excessively gathered most objects into a huge cluster. Quantitative evaluation using four indicators, including the silhouette, the R-squared index, the Davis–Bouldin index, and the clustering scheme quality index, indicated that the NS-DBSCAN algorithm was superior to the hierarchical clustering and NC_DT algorithms.
Automated Multi-Sensor 3D Reconstruction for the Web
Authors: Julin Arttu , Jaalama Kaisa , Virtanen Juho-Pekka , Maksimainen Mikko , Kurkela Matti , Hyyppä Juha , Hyyppä Hannu
Published: May 2019

The Internet has become a major dissemination and sharing platform for 3D content. The utilization of 3D measurement methods can drastically increase the production efficiency of 3D content in an increasing number of use cases where 3D documentation of real-life objects or environments is required. We demonstrated a developed, highly automated and integrated content creation process of providing reality-based photorealistic 3D models for the web. Close-range photogrammetry, terrestrial laser scanning (TLS) and their combination are compared using available state-of-the-art tools in a real-life project setting with real-life limitations. Integrating photogrammetry and TLS is a good compromise for both geometric and texture quality. Compared to approaches using only photogrammetry or TLS, it is slower and more resource-heavy but combines complementary advantages of each method, such as direct scale determination from TLS or superior image quality typically used in photogrammetry. The integration is not only beneficial, but clearly productionally possible using available state-of-the-art tools that have become increasingly available also for non-expert users. Despite the high degree of automation, some manual editing steps are still required in practice to achieve satisfactory results in terms of adequate visual quality. This is mainly due to the current limitations of WebGL technology.
The Spatial Equity of Nursing Homes in Changchun: A Multi-Trip Modes Analysis
Authors: Hu Shuju , Song Wei , Li Chenggu , Lu Jia
Published: May 2019

Based on network analysis, different trip modes were integrated into an improved potential model, and the geography of the spatial equity of nursing homes in Changchun is explored in 5-min, 10-min and 15-min scenarios, respectively. Results show that: (1) trip modes have significant influence on spatial equity and that the geography of spatial equity varied with trip modes; (2) the spatial equity value in Changchun is overall kept to a very low level. Most areas in urban fringes and urban core areas belong to underserved areas, and the capacity of nursing home, travel cost and the number of seniors, are the main influencing factors; (3) the geography of spatial equity in different scenarios show a very similar ring structure; namely, the spatial equity value within the urban core and at the most urban periphery is lower than that in intermediate areas. The hot spot analysis showed that the southwest urban fringes and east of the urban core are hot spot areas, while the urban core itself has cold spot areas.
A Convenient Tool for District Heating Route Optimization Based on Parallel Ant Colony System Algorithm and 3D WebGIS
Authors: Zhang Yang , Zhang Guoyong , Zhao Huihui , Cao Yuming , Liu Qinhuo , Shen Zhanfeng , Li Aimin
Published: May 2019

In a district heating engineering project, the design of the heating route is an indispensable but laborious process. This paper proposes a planning indicator to measure the suitability of a candidate heating route, and provides an intelligent method and a convenient tool for the preliminary design of the district heating route. The Fengrun heating engineering project was chosen as a case study. The remote sensing imagery and OpenStreetMap were used as the data sources. First, the remote sensing imagery was classified into five classes and converted into binary images. Second, the district heating route planning indicator was defined based on the cost function. The cost function and the updating strategy of the ant colony system algorithm were modified according to the heating route selection requirement. Additionally, the parallel computing technology was adopted to improve the efficiency. With the help of the open source Cesium engine and the three-dimensional (3D) WebGIS technology, an interactive route design platform that combined our algorithm was finally provided. The optimum routes by the platform were compared to the corresponding sequential algorithm, the route selected manually, as well as the commercial ArcGIS platform. The proposed algorithm can get 28 candidate routes with better indicator values than the manually selected route. Compared to the corresponding sequential algorithm, our algorithm improved the efficiency by 4.789 times. The proposed 3D WebGIS tool is more applicable and user-friendly for the heating route design.
GIS Mapping of Driving Behavior Based on Naturalistic Driving Data
Authors: Balsa-Barreiro José , Valero-Mora Pedro M. , Berné-Valero José L. , Varela-García Fco-Alberto
Published: May 2019

Naturalistic driving can generate huge datasets with great potential for research. However, to analyze the collected data in naturalistic driving trials is quite complex and difficult, especially if we consider that these studies are commonly conducted by research groups with somewhat limited resources. It is quite common that these studies implement strategies for thinning and/or reducing the data volumes that have been initially collected. Thus, and unfortunately, the great potential of these datasets is significantly constrained to specific situations, events, and contexts. For this, to implement appropriate strategies for the visualization of these data is becoming increasingly necessary, at any scale. Mapping naturalistic driving data with Geographic Information Systems (GIS) allows for a deeper understanding of our driving behavior, achieving a smarter and broader perspective of the whole datasets. GIS mapping allows for many of the existing drawbacks of the traditional methodologies for the analysis of naturalistic driving data to be overcome. In this article, we analyze which are the main assets related to GIS mapping of such data. These assets are dominated by the powerful interface graphics and the great operational capacity of GIS software.
Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum)
Authors: Sun Xiaorong , Shu Jinshuai , Ali Mohamed Ali Mohamed , Deng Xuebin , Zhi Xiaona , Bai Jinrui , Cui Yanan , Lu Xiaoxiao , Du Yongchen , Wang Xiaoxuan , Huang Zejun , Guo Yanmei , Liu Lei , Li Junming
Published: May 2019

Internode length is an important agronomic trait affecting plant architecture and crop yield. However, few genes for internode elongation have been identified in tomato. In this study, we characterized an elongated internode inbred line P502, which is a natural mutant of the tomato cultivar 05T606. The mutant P502 exhibits longer internode and higher bioactive GA concentration compared with wild-type 05T606. Genetic analysis suggested that the elongated internode trait is controlled by quantitative trait loci (QTL). Then, we identified a major QTL on chromosome 2 based on molecular markers and bulked segregant analysis (BSA). The locus was designated as EI (Elongated Internode), which explained 73.6% genetic variance. The EI was further mapped to a 75.8-kb region containing 10 genes in the reference Heinz 1706 genome. One single nucleotide polymorphism (SNP) in the coding region of solyc02g080120.1 was identified, which encodes gibberellin 2-beta-dioxygenase 7 (SlGA2ox7). SlGA2ox7, orthologous to AtGA2ox7 and AtGA2ox8, is involved in the regulation of GA degradation. Overexpression of the wild EI gene in mutant P502 caused a dwarf phenotype with a shortened internode. The difference of EI expression levels was not significant in the P502 and wild-type, but the expression levels of GA biosynthetic genes including CPS, KO, KAO, GA20ox1, GA20ox2, GA20ox4, GA3ox1, GA2ox1, GA2ox2, GA2ox4, and GA2ox5, were upregulated in mutant P502. Our results may provide a better understanding of the genetics underlying the internode elongation and valuable information to improve plant architecture of the tomato.
Molecular Modeling-Guided Design of Phospholipid-Based Prodrugs
Authors: Markovic Milica , Ben-Shabat Shimon , Keinan Shahar , Aponick Aaron , Zimmermann Ellen M. , Dahan Arik
Published: May 2019

The lipidic prodrug approach is an emerging field for improving a number of biopharmaceutical and drug delivery aspects. Owing to their structure and nature, phospholipid (PL)-based prodrugs may join endogenous lipid processing pathways, and hence significantly improve the pharmacokinetics and/or bioavailability of the drug. Additional advantages of this approach include drug targeting by enzyme-triggered drug release, blood–brain barrier permeability, lymphatic targeting, overcoming drug resistance, or enabling appropriate formulation. The PL-prodrug design includes various structural modalities-different conjugation strategies and/or the use of linkers between the PL and the drug moiety, which considerably influence the prodrug characteristics and the consequent effects. In this article, we describe how molecular modeling can guide the structural design of PL-based prodrugs. Computational simulations can predict the extent of phospholipase A2 (PLA2)-mediated activation, and facilitate prodrug development. Several computational methods have been used to facilitate the design of the pro-drugs, which will be reviewed here, including molecular docking, the free energy perturbation method, molecular dynamics simulations, and free density functional theory. Altogether, the studies described in this article indicate that computational simulation-guided PL-based prodrug molecular design correlates well with the experimental results, allowing for more mechanistic and less empirical development. In the future, the use of molecular modeling techniques to predict the activity of PL-prodrugs should be used earlier in the development process.
Molecular Signature of Prospero Homeobox 1 (PROX1) in Follicular Thyroid Carcinoma Cells
Authors: Rudzińska Magdalena , Grzanka Małgorzata , Stachurska Anna , Mikula Michał , Paczkowska Katarzyna , Stępień Tomasz , Paziewska Agnieszka , Ostrowski Jerzy , Czarnocka Barbara
Published: May 2019

The prospero homeobox 1 (PROX1) transcription factor is a product of one of the lymphangiogenesis master genes. It has also been suggested to play a role in carcinogenesis, although its precise role in tumour development and metastasis remains unclear. The aim of this study was to gain more knowledge on the PROX1 function in thyroid tumorigenesis. Follicular thyroid cancer-derived cells—CGTH-W-1—were transfected with PROX1-siRNA (small interfering RNA) and their proliferation, cell cycle, apoptosis and motility were then analysed. The transcriptional signature of PROX1 depletion was determined using RNA-Sequencing (RNA-Seq) and the expression of relevant genes was further validated using reverse transcriptase quantitative PCR (RT-qPCR), Western blot and immunocytochemistry. PROX1 depletion resulted in a decreased cell motility, with both migratory and invasive potential being significantly reduced. The cell morphology was also affected, while the other studied cancer-related cell characteristics were not significantly altered. RNA-seq analysis revealed significant changes in the expression of transcripts encoding genes involved in both motility and cytoskeleton organization. Our transcriptional analysis of PROX1-depleted follicular thyroid carcinoma cells followed by functional and phenotypical analyses provide, for the first time, evidence that PROX1 plays an important role in the metastasis of thyroid cancer cells by regulating genes involved in focal adhesion and cytoskeleton organization in tumour cells.
PgMYB2, a MeJA-Responsive Transcription Factor, Positively Regulates the Dammarenediol Synthase Gene Expression in Panax Ginseng
Authors: Liu Tuo , Luo Tiao , Guo Xiangqian , Zou Xian , Zhou Donghua , Afrin Sadia , Li Gui , Zhang Yue , Zhang Ru , Luo Zhiyong
Published: May 2019

The MYB transcription factor family members have been reported to play different roles in plant growth regulation, defense response, and secondary metabolism. However, MYB gene expression has not been reported in Panax ginseng. In this study, we isolated a gene from ginseng adventitious root, PgMYB2, which encodes an R2R3-MYB protein. Subcellular localization revealed that PgMYB2 protein was exclusively detected in the nucleus of Allium cepa epidermis. The highest expression level of PgMYB2 was found in ginseng root and it was significantly induced by plant hormones methyl jasmonate (MeJA). Furthermore, the binding interaction between PgMYB2 protein and the promoter of dammarenediol synthase (DDS) was found in the yeast strain Y1H Gold. Moreover, the electrophoretic mobility shift assay (EMSA) identified the binding site of the interaction and the results of transiently overexpressing PgMYB2 in plants also illustrated that it may positively regulate the expression of PgDDS. Based on the key role of PgDDS gene in ginsenoside synthesis, it is reasonable to believe that this report will be helpful for the future studies on the MYB family in P. ginseng and ultimately improving the ginsenoside production through genetic and metabolic engineering.
HER2 Upregulates ATF4 to Promote Cell Migration via Activation of ZEB1 and Downregulation of E-Cadherin
Authors: Zeng Peng , Sun Shengnan , Li Rui , Xiao Zhi-Xiong , Chen Hu
Published: May 2019

HER2 (human epidermal growth factor receptor 2) activation is critical in breast cancer development. HER2 promotes cell proliferation, angiogenesis, survival, and metastasis by activation of PI3K/Akt, Ras/MEK/ERK, and JAK/STAT pathways. However, beyond these signaling molecules, the key proteins underlining HER2-mediated metastasis remain elusive. ATF4 (Activating transcription factor 4), a critical regulator in unfolded protein response (UPR), is implicated in cell migration and tumor metastasis. In this study, we demonstrate that HER2 upregulated ATF4 expression at both mRNA and protein levels, resulting in cell migration increased. In addition, ATF4 upregulated ZEB1 (Zinc finger E-box-binding homeobox 1) and suppressed E-cadherin expression resulting in promoting cell migration. Restoration of E-cadherin expression effectively inhibited HER2- or ATF4-mediated cell migration. In addition, upregulated expression of ATF4 was found in HER2-positive breast cancer specimens. Together, this study demonstrates that ATF4-ZEB1 is important for HER2-mediated cell migration and suggests that ATF4-ZEB1 may be potential therapeutic targets for breast cancer metastasis.
Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer
Authors: Satoh Tadashi , Yagi-Utsumi Maho , Okamoto Kenta , Kurimoto Eiji , Tanaka Keiji , Kato Koichi
Published: May 2019

The 26S proteasome is critical for the selective degradation of proteins in eukaryotic cells. This enzyme complex is composed of approximately 70 subunits, including the structurally homologous proteins α1–α7, which combine to form heptameric rings. The correct arrangement of these α subunits is essential for the function of the proteasome, but their assembly does not occur autonomously. Assembly of the α subunit is assisted by several chaperones, including the PAC3-PAC4 heterodimer. In this study we showed that the PAC3-PAC4 heterodimer functions as a molecular matchmaker, stabilizing the α4-α5-α6 subcomplex during the assembly of the α-ring. We solved a 0.96-Å atomic resolution crystal structure for a PAC3 homodimer which, in conjunction with nuclear magnetic resonance (NMR) data, highlighted the mobility of the loop comprised of residues 51 to 61. Based on these structural and dynamic data, we created a three-dimensional model of the PAC3-4/α4/α5/α6 quintet complex, and used this model to investigate the molecular and structural basis of the mechanism of proteasome α subunit assembly, as mediated by the PAC3-PAC4 heterodimeric chaperone. Our results provide a potential basis for the development of selective inhibitors against proteasome biogenesis.
The Structural Biology of Bcl-xL
Authors: Lee Erinna F. , Fairlie W. Douglas
Published: May 2019

Interactions between the pro-survival and pro-apoptotic members of the Bcl-2 family of proteins dictate whether a cell lives or dies. Much of our knowledge of the molecular details of these interactions has come from biochemical and structural studies on the pro-survival protein Bcl-xL. The first high-resolution structure of any Bcl-2 family member was of Bcl-xL, which revealed the conserved topology amongst all family members. Subsequent structures of Bcl-xL complexes with pro-apoptotic ligands demonstrated the general features of all pro-survival:pro-apoptotic complexes. Structural studies involving Bcl-xL were also the basis for the discovery of the first small-molecule pro-survival protein inhibitors, leading ultimately to the development of a new class of drugs now successfully used for cancer treatment in the clinic. This article will review our current knowledge of the structural biology of Bcl-xL and how this has impacted our understanding of the molecular details of the intrinsic apoptotic pathway.
Characterization of a New Reconstructed Full Thickness Skin Model, T-Skin™, and its Application for Investigations of Anti-Aging Compounds
Authors: Bataillon Michel , Lelièvre Damien , Chapuis Adeline , Thillou Fabienne , Autourde Jean Baptiste , Durand Steven , Boyera Nathalie , Rigaudeau Anne-Sophie , Besné Isabelle , Pellevoisin Christian
Published: May 2019

Background: We have characterized a new reconstructed full-thickness skin model, T-Skin™, compared to normal human skin (NHS) and evaluated its use in testing anti-aging compounds. Methods: The structure and layer-specific markers were compared with NHS using histological and immunohistological staining. In anti-aging experiments, T-SkinTM was exposed to retinol (10 µM) or vitamin C (200 µM) for 5 days, followed by immunohistological staining evaluation. Results: T-Skin™ exhibits a well stratified, differentiated and self-renewing epidermis with a dermal compartment of functional fibroblasts. Epidermal (cytokeratin 10, transglutaminase 1), dermo–epidermal junction (DEJ) (laminin 5, collagen-IV, collagen VII) and dermally-located (fibrillin 1, procollagen I) biomarkers were similar to those in NHS. Treatment of T-Skin™ with retinol decreased the expression of differentiation markers, cytokeratin 10 and transglutaminase 1 and increased the proliferation marker, Ki67, in epidermis basal-layer cells. Vitamin C increased the expression of DEJ components, collagen IV and VII and dermal procollagen 1. Conclusions: T-Skin™ exhibits structural and biomarker location characteristics similar to NHS. Responses of T-Skin™ to retinol and vitamin C treatment were consistent with those of their known anti-aging effects. T-Skin™ is a promising model to investigate responses of epidermal, DEJ and dermal regions to new skin anti-ageing compounds.
Immunoepigenetics Combination Therapies: An Overview of the Role of HDACs in Cancer Immunotherapy
Authors: Banik Debarati , Moufarrij Sara , Villagra Alejandro
Published: May 2019

Long-standing efforts to identify the multifaceted roles of histone deacetylase inhibitors (HDACis) have positioned these agents as promising drug candidates in combatting cancer, autoimmune, neurodegenerative, and infectious diseases. The same has also encouraged the evaluation of multiple HDACi candidates in preclinical studies in cancer and other diseases as well as the FDA-approval towards clinical use for specific agents. In this review, we have discussed how the efficacy of immunotherapy can be leveraged by combining it with HDACis. We have also included a brief overview of the classification of HDACis as well as their various roles in physiological and pathophysiological scenarios to target key cellular processes promoting the initiation, establishment, and progression of cancer. Given the critical role of the tumor microenvironment (TME) towards the outcome of anticancer therapies, we have also discussed the effect of HDACis on different components of the TME. We then have gradually progressed into examples of specific pan-HDACis, class I HDACi, and selective HDACis that either have been incorporated into clinical trials or show promising preclinical effects for future consideration. Finally, we have included examples of ongoing trials for each of the above categories of HDACis as standalone agents or in combination with immunotherapeutic approaches.
Transcriptomic Analysis Reveals Priming of The Host Antiviral Interferon Signaling Pathway by Bronchobini® Resulting in Balanced Immune Response to Rhinovirus Infection in Mouse Lung Tissue Slices
Authors: Reamon-Buettner Stella Marie , Niehof Monika , Hirth Natalie , Danov Olga , Obernolte Helena , Braun Armin , Warnecke Jürgen , Sewald Katherina , Wronski Sabine
Published: May 2019

Rhinovirus (RV) is the predominant virus causing respiratory tract infections. Bronchobini® is a low dose multi component, multi target preparation used to treat inflammatory respiratory diseases such as the common cold, described to ease severity of symptoms such as cough and viscous mucus production. The aim of the study was to assess the efficacy of Bronchobini® in RV infection and to elucidate its mode of action. Therefore, Bronchobini®’s ingredients (BRO) were assessed in an ex vivo model of RV infection using mouse precision-cut lung slices, an organotypic tissue capable to reflect the host immune response to RV infection. Cytokine profiles were assessed using enzyme-linked immunosorbent assay (ELISA) and mesoscale discovery (MSD). Gene expression analysis was performed using Affymetrix microarrays and ingenuity pathway analysis. BRO treatment resulted in the significant suppression of RV-induced antiviral and pro-inflammatory cytokine release. Transcriptome analysis revealed a multifactorial mode of action of BRO, with a strong inhibition of the RV-induced pro-inflammatory and antiviral host response mediated by nuclear factor kappa B (NFkB) and interferon signaling pathways. Interestingly, this was due to priming of these pathways in the absence of virus. Overall, BRO exerted its beneficial anti-inflammatory effect by priming the antiviral host response resulting in a reduced inflammatory response to RV infection, thereby balancing an otherwise excessive inflammatory response.
Illumina® Sequencing Reveals Candidate Genes of Carotenoid Metabolism in Three Pummelo Cultivars (Citrus Maxima) with Different Pulp Color
Authors: Jiang Cui-Cui , Zhang Yan-Fang , Lin Yan-Jin , Chen Yuan , Lu Xin-Kun
Published: May 2019

Pummelo (Citrus maxima) is one of important fruit trees, which belongs to Citrus species. The fruits of different pummelo cultivars have different colors and differ in the contents of carotenoid. Our results clearly showed that ‘Huangjinmiyou’ (HJMY) has the highest content of β-carotene, followed by ‘Hongroumiyou’ (HRMY) and ‘Guanximiyou’ (GXMY). Lycopene is dominantly accumulated in HRMY. However, the molecular mechanism underlying the carotenoid accumulation in pummelo flesh is not fully understood. In this study, we used the RNA-Seq technique to investigate the candidate genes of carotenoid metabolism in the flesh of pummelo cv. GXMY and its mutants HRMY and HJMY in three development periods of fruit. After data assembly and bioinformatic analysis, a total of 357 genes involved in biosynthesis of secondary metabolites were isolated, of which 12 differentially expressed genes (DEGs) are involved in carotenoid biosynthesis. Among these 12 DEGs, phytoene synthase (PSY2), lycopene β-cyclase (LYCB2), lycopene Ɛ-cyclase (LYCE), carotenoid cleavage dioxygenases (CCD4), 9-cis-epoxycarotenoid dioxygenase (NCED2), aldehyde oxidase 3 (AAO3), and ABA 8′-hydroxylases (CYP707A1) are the most distinct DEGs in three pummelo cultivars. The co-expression analysis revealed that the expression patterns of several transcription factors such as bHLH, MYB, ERF, NAC and WRKY are highly correlated with DEGs, which are involved in carotenoid biosynthesis. In addition, the expression patterns of 22 DEGs were validated by real-time quantitative PCR (RT-qPCR) and the results are highly concordant with the RNA-Seq results. Our results provide a global vision of transcriptomic profile among three pummelo cultivars with different pulp colors. These results would be beneficial to further study the molecular mechanism of carotenoid accumulation in pummelo flesh and help the breeding of citrus with high carotenoid content.
Mechanisms of the Metabolic Shift during Somatic Cell Reprogramming
Authors: Nishimura Ken , Fukuda Aya , Hisatake Koji
Published: May 2019

Pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), hold a huge promise for regenerative medicine, drug development, and disease modeling. PSCs have unique metabolic features that are akin to those of cancer cells, in which glycolysis predominates to produce energy as well as building blocks for cellular components. Recent studies indicate that the unique metabolism in PSCs is not a mere consequence of their preference for a low oxygen environment, but is an active process for maintaining self-renewal and pluripotency, possibly in preparation for rapid response to the metabolic demands of differentiation. Understanding the regulatory mechanisms of this unique metabolism in PSCs is essential for proper derivation, generation, and maintenance of PSCs. In this review, we discuss the metabolic features of PSCs and describe the current understanding of the mechanisms of the metabolic shift during reprogramming from somatic cells to iPSCs, in which the metabolism switches from oxidative phosphorylation (OxPhos) to glycolysis.
Relationship of Iron Metabolism and Short-Term Cuprizone Treatment of C57BL/6 Mice
Authors: Pandur Edina , Pap Ramóna , Varga Edit , Jánosa Gergely , Komoly Sámuel , Fórizs Judit , Sipos Katalin
Published: May 2019

One of the models to investigate the distinct mechanisms contributing to neurodegeneration in multiple sclerosis is based on cuprizone (CZ) intoxication. CZ is toxic to mature oligodendrocytes and produces demyelination within the central nervous system but does not cause direct neuronal damage. The CZ model is suitable for better understanding the molecular mechanism of de- and remyelination processes of oligodendrocytes. CZ is a copper chelating agent and it also affects the iron metabolism in brain and liver tissues. To determine the early effect of CZ treatment on iron homeostasis regulation, cytosolic and mitochondrial iron storage, as well as some lipid metabolism genes, we investigated the expression of respective iron homeostasis and lipid metabolism genes of the corpus callosum (CC) and the liver after short-term CZ administration. In the present study C57BL/6 male mice aged four weeks were fed with standard rodent food premixed with 0.2 w/w% CZ for two or eight days. The major findings of our experiments are that short-term CZ treatment causes significant changes in iron metabolism regulation as well as in the expression of myelin and lipid synthesis-related genes, even before apparent demyelination occurs. Both in the CC and the liver the iron uptake, utilization and storage are modified, though not always the same way or to the same extent in the two organs. Understanding the role of iron in short-term and long-term CZ intoxication could provide a partial explanation of the discrepant signs of acute and chronic MS. These could contribute to understanding the development of multiple sclerosis and might provide a possible drug target.
Immune Checkpoint Blockade for Advanced NSCLC: A New Landscape for Elderly Patients
Authors: Perrotta Fabio , Rocco Danilo , Vitiello Fabiana , De Palma Raffaele , Guerra Germano , De Luca Antonio , Navani Neal , Bianco Andrea
Published: May 2019

The therapeutic scenario for elderly patients with advanced NSCLC has been limited to radiotherapy and chemotherapy. Recently, a novel therapeutic approach based on targeting the immune-checkpoints has showed noteworthy results in advanced NSCLC. PD1/PD-L1 pathway is co-opted by tumor cells through the expression of PD-L1 on the tumor cell surface and on cells within the microenvironment, leading to suppression of anti-tumor cytolytic T-cell activity by the tumor. The success of immune-checkpoints inhibitors in clinical trials led to rapid approval by the FDA and EMA. Currently, data regarding efficacy and safety of ICIs in older subjects is limited by the poor number of elderly recruited in clinical trials. Careful assessment and management of comorbidities is essential to achieve better outcomes and limit the immune related adverse events in elderly NSCLC patients.
CADM1, MAL, and miR124 Promoter Methylation as Biomarkers of Transforming Cervical Intrapithelial Lesions
Authors: del Pino Marta , Sierra Adriana , Marimon Lorena , Martí Delgado Cristina , Rodriguez-Trujillo Adriano , Barnadas Esther , Saco Adela , Torné Aureli , Ordi Jaume
Published: May 2019

Background: Squamous intraepithelial lesions/cervical intraepithelial neoplasias (SIL/CIN) are high-risk human papilloma virus (hrHPV)-related lesions which are considered as high grade (HSIL/CIN2-3) or low grade (LSIL/CIN1) lesions according to their risk of progression to cervical cancer (CC). Most HSIL/CIN2-3 are considered as transforming hrHPV infections, so truly CC precursors, although some clear spontaneously. hrHPV testing has a high sensitivity for the detection of HSIL/CIN2-3 but a relatively low specificity for identifying transforming lesions. We aimed to determine whether the combination of CADM1, MAL and miR124 promoter methylation status assessed in histological samples can be used as a biomarker in the identification of transforming HSIL/CIN lesions. Design: 131 cervical biopsies, including 8 cases with no lesion and a negative hrHPV test result (control group), 19 low-grade (L)SIL/CIN1, 30 HSIL/CIN2, 60 HSIL/CIN3, and 14 CC were prospectively collected. hrHPV was detected and genotyped using the polymerase chain reaction (PCR)-based technique SPF10 HPV LIPA. A multiplex quantitative methylation-specific PCR (qMSP) was used to identify the methylation status of the CADM1, MAL, and miR124 promoter genes. Results: Significantly higher methylation levels of CADM1, MAL and miR-124 were found in HSIL/CIN2-3 and CC compared with normal and LSIL lesions. DNA methylation of at least one gene was detected in 12.5% (1/8) of normal samples, 31.5% (6/19) of LSIL/CIN1, 83.3% (25/30) of HSIL/CIN2, 81.6% (49/60) of HSIL/CIN3 and 100% (14/14) of CC (p < 0.001). The sensitivity and specificity for HSIL/CIN2-3 and CC of having at least one methylated gene were 84.6% and 74.0%, respectively. The sensitivity and specificity of the combination of at least one methylated gene and a positive hrHPV test were 80.7% and 85.1% for HSIL/CIN2-3 and CC, respectively. Conclusions: The methylation rate of CADM1, MAL and miR124 increases with the severity of the lesion. Further research is warranted to evaluate the usefulness of these biomarkers for the identification of transforming HSIL/CIN.
Ion Channels Involved in Tooth Pain
Authors: Lee Kihwan , Lee Byeong-Min , Park Chul-Kyu , Kim Yong Ho , Chung Gehoon
Published: May 2019

The tooth has an unusual sensory system that converts external stimuli predominantly into pain, yet its sensory afferents in teeth demonstrate cytochemical properties of non-nociceptive neurons. This review summarizes the recent knowledge underlying this paradoxical nociception, with a focus on the ion channels involved in tooth pain. The expression of temperature-sensitive ion channels has been extensively investigated because thermal stimulation often evokes tooth pain. However, temperature-sensitive ion channels cannot explain the sudden intense tooth pain evoked by innocuous temperatures or light air puffs, leading to the hydrodynamic theory emphasizing the microfluidic movement within the dentinal tubules for detection by mechanosensitive ion channels. Several mechanosensitive ion channels expressed in dental sensory systems have been suggested as key players in the hydrodynamic theory, and TRPM7, which is abundant in the odontoblasts, and recently discovered PIEZO receptors are promising candidates. Several ligand-gated ion channels and voltage-gated ion channels expressed in dental primary afferent neurons have been discussed in relation to their potential contribution to tooth pain. In addition, in recent years, there has been growing interest in the potential sensory role of odontoblasts; thus, the expression of ion channels in odontoblasts and their potential relation to tooth pain is also reviewed.
Vectisol Formulation Enhances Solubility of Resveratrol and Brings Its Benefits to Kidney Transplantation in a Preclinical Porcine Model
Authors: Soussi David , Danion Jérôme , Baulier Edouard , Favreau Frédéric , Sauvageon Ysé , Bossard Valentin , Matillon Xavier , Turpin Frédéric , Belgsir El Mustapha , Thuillier Raphaël , Hauet Thierry
Published: May 2019

Current organ shortages have led centers to extend the acceptance criteria for organs, increasing the risk for adverse outcomes. Current preservation protocols have not been adapted so as to efficiently protect these organs. Herein, we target oxidative stress, the key mechanism of ischemia reperfusion injury. Vectisol® is a novel antioxidant strategy based on the encapsulation of resveratrol into a cyclodextrin, increasing its bioavailability. We tested this compound as an additive to the most popular static preservation solutions and machine perfusion (LifePort) in a preclinical pig model of kidney autotransplantation. In regard to static preservation, supplementation improved glomerular filtration and proximal tubular function early recovery. Extended follow-up confirmed the higher level of protection, slowing chronic loss of function (creatininemia and proteinuria) and the onset of histological lesions. Regarding machine perfusion, the use of Vectisol® decreased oxidative stress and apoptosis at the onset of reperfusion (30 min post declamping). Improved quality was confirmed with decreased early levels of circulating SOD (Superoxide Dismutase) and ASAT (asparagine amino transferase). Supplementation slowed the onset of chronic loss of function, as well as interstitial fibrosis and tubular atrophy. The simple addition of Vectisol® to the preservation solution significantly improved the performance of organ preservation, with long-term effects on the outcome. This strategy is thus a key player for future multi-drug therapy aimed at ischemia reperfusion in transplantation.
Uremic Toxin Lanthionine Interferes with the Transsulfuration Pathway, Angiogenetic Signaling and Increases Intracellular Calcium
Authors: Vigorito Carmela , Anishchenko Evgeniya , Mele Luigi , Capolongo Giovanna , Trepiccione Francesco , Zacchia Miriam , Lombari Patrizia , Capasso Rosanna , Ingrosso Diego , Perna Alessandra F.
Published: May 2019

(1) The beneficial effects of hydrogen sulfide (H2S) on the cardiovascular and nervous system have recently been re-evaluated. It has been shown that lanthionine, a side product of H2S biosynthesis, previously used as a marker for H2S production, is dramatically increased in circulation in uremia, while H2S release is impaired. Thus, lanthionine could be classified as a novel uremic toxin. Our research was aimed at defining the mechanism(s) for lanthionine toxicity. (2) The effect of lanthionine on H2S release was tested by a novel lead acetate strip test (LAST) in EA.hy926 cell cultures. Effects of glutathione, as a redox agent, were assayed. Levels of sulfane sulfur were evaluated using the SSP4 probe and flow cytometry. Protein content and glutathionylation were analyzed by Western Blotting and immunoprecipitation, respectively. Gene expression and miRNA levels were assessed by qPCR. (3) We demonstrated that, in endothelial cells, lanthionine hampers H2S release; reduces protein content and glutathionylation of transsulfuration enzyme cystathionine-β-synthase; modifies the expression of miR-200c and miR-423; lowers expression of vascular endothelial growth factor VEGF; increases Ca2+ levels. (4) Lanthionine-induced alterations in cell cultures, which involve both sulfur amino acid metabolism and calcium homeostasis, are consistent with uremic dysfunctional characteristics and further support the uremic toxin role of this amino acid.
Group 2 Innate Lymphoid Cells (ILC2): Type 2 Immunity and Helminth Immunity
Authors: Herbert De’Broski , Douglas Bonnie , Zullo Kelly
Published: May 2019

Group 2 innate lymphoid cells (ILC2) have emerged as a major component of type 2 inflammation in mice and humans. ILC2 secrete large amounts of interleukins 5 and 13, which are largely responsible for host protective immunity against helminth parasites because these cytokines induce profound changes in host physiology that include: goblet cell metaplasia, mucus accumulation, smooth muscle hypercontractility, eosinophil and mast cell recruitment, and alternative macrophage activation (M2). This review covers the initial recognition of ILC2 as a distinct cell lineage, the key studies that established their biological importance, particularly in helminth infection, and the new directions that are likely to be the focus of emerging work that further explores this unique cell population in the context of health and disease.
LncRNA HOTAIR in Tumor Microenvironment: What Role?
Authors: Botti Gerardo , Scognamiglio Giosuè , Aquino Gabriella , Liguori Giuseppina , Cantile Monica
Published: May 2019

lncRNAs participate in many cellular processes, including regulation of gene expression at the transcriptional and post-transcriptional levels. In addition, many lncRNAs can contribute to the development of different human diseases including cancer. The tumor microenvironment (TME) plays an important role during tumor growth and metastatic progression, and most of these lncRNAs have a key function in TME intracellular signaling. Among the numerous identified lncRNAs, several experimental evidences have shown the fundamental role of the lncRNA HOTAIR in carcinogenesis, also highlighting its use as a circulating biomarker. In this review we described the contribution of HOTAIR in the TME modulation, highlighting its relation with cellular and non-cellular components during tumor evolution and progression.
Effect of Indoxyl Sulfate on the Repair and Intactness of Intestinal Epithelial Cells: Role of Reactive Oxygen Species’ Release
Authors: Adesso Simona , Ruocco Marco , Rapa Shara Francesca , Dal Piaz Fabrizio , Di Iorio Biagio Raffaele , Popolo Ada , Autore Giuseppina , Nishijima Fuyu , Pinto Aldo , Marzocco Stefania
Published: May 2019

Chronic kidney disease (CKD) is characterized by an oxidative stress status, driving some CKD-associated complications, even at the gastrointestinal level. Indoxyl Sulfate (IS) is a protein-bound uremic toxin, poorly eliminated by dialysis. This toxin is able to affect the intestinal system, but its molecular mechanism/s in intestinal epithelial cells (IECs) remain poorly understood. This study’s aim was to evaluate the effect of IS (31.2–250 µM) on oxidative stress in IEC-6 cells and on the intactness of IECs monolayers. Our results indicated that IS enhanced oxidative cell damage by inducing reactive oxygen species (ROS) release, reducing the antioxidant response and affecting Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) nuclear translocation as well its related antioxidant enzymes. In the wound healing assay model, IS reduced IEC-6 migration, slightly impaired actin cytoskeleton rearrangement; this effect was associated with connexin 43 alteration. Moreover, we reported the effect of CKD patients’ sera in IEC-6 cells. Our results indicated that patient sera induced ROS release in IEC-6 cells directly related to IS sera content and this effect was reduced by AST-120 serum treatment. Results highlighted the effect of IS in inducing oxidative stress in IECs and in impairing the intactness of the IECs cell monolayer, thus significantly contributing to CKD-associated intestinal alterations.
Exogenous RNAs for Gene Regulation and Plant Resistance
Authors: Dubrovina Alexandra S. , Kiselev Konstantin V.
Published: May 2019

Recent investigations documented that plants can uptake and process externally applied double-stranded RNAs (dsRNAs), hairpin RNAs (hpRNAs), and small interfering RNAs (siRNAs) designed to silence important genes of plant pathogenic viruses, fungi, or insects. The exogenously applied RNAs spread locally and systemically, move into the pathogens, and induce RNA interference-mediated plant pathogen resistance. Recent findings also provided examples of plant transgene and endogene post-transcriptional down-regulation by complementary dsRNAs or siRNAs applied onto the plant surfaces. Understanding the plant perception and processing of exogenous RNAs could result in the development of novel biotechnological approaches for crop protection. This review summarizes and discusses the emerging studies reporting on exogenous RNA applications for down-regulation of essential fungal and insect genes, targeting of plant viruses, or suppression of plant transgenes and endogenes for increased resistance and changed phenotypes. We also analyze the current understanding of dsRNA uptake mechanisms and dsRNA stability in plant environments.
Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant
Authors: Teo Seng Chong , Liew Kok Jun , Shamsir Mohd Shahir , Chong Chun Shiong , Bruce Neil C. , Chan Kok-Gan , Goh Kian Mau
Published: May 2019

A halo-thermophilic bacterium, Roseithermus sacchariphilus strain RA (previously known as Rhodothermaceae bacterium RA), was isolated from a hot spring in Langkawi, Malaysia. A complete genome analysis showed that the bacterium harbors 57 glycoside hydrolases (GHs), including a multi-domain xylanase (XynRA2). The full-length XynRA2 of 813 amino acids comprises a family 4_9 carbohydrate-binding module (CBM4_9), a family 10 glycoside hydrolase catalytic domain (GH10), and a C-terminal domain (CTD) for type IX secretion system (T9SS). This study aims to describe the biochemical properties of XynRA2 and the effects of CBM truncation on this xylanase. XynRA2 and its CBM-truncated variant (XynRA2ΔCBM) was expressed, purified, and characterized. The purified XynRA2 and XynRA2ΔCBM had an identical optimum temperature at 70 °C, but different optimum pHs of 8.5 and 6.0 respectively. Furthermore, XynRA2 retained 94% and 71% of activity at 4.0 M and 5.0 M NaCl respectively, whereas XynRA2ΔCBM showed a lower activity (79% and 54%). XynRA2 exhibited a turnover rate (kcat) of 24.8 s−1, but this was reduced by 40% for XynRA2ΔCBM. Both the xylanases hydrolyzed beechwood xylan predominantly into xylobiose, and oat-spelt xylan into a mixture of xylo-oligosaccharides (XOs). Collectively, this work suggested CBM4_9 of XynRA2 has a role in enzyme performance.