bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular prostaglandin E2 contributes to hypoxia-induced proximal tubular cell death
Authors: García-Pastor Coral , Benito-Martínez Selma , Bosch Ricardo J. , Fernández-Martínez Ana B. , Lucio-Cazaña Francisco J. 
Published: March 2021

AbstractProximal tubular cells (PTC) are particularly vulnerable to hypoxia-induced apoptosis, a relevant factor for kidney disease. We hypothesized here that PTC death under hypoxia is mediated by cyclo-oxygenase (COX-2)-dependent production of prostaglandin E2 (PGE2), which was confirmed in human proximal tubular HK-2 cells because hypoxia (1% O2)-induced apoptosis (i) was prevented by a COX-2 inhibitor and by antagonists of prostaglandin (EP) receptors and (ii) was associated to an increase in intracellular PGE2 (iPGE2) due to hypoxia-inducible factor-1α-dependent transcriptional up-regulation of COX-2. Apoptosis was also prevented by inhibitors of the prostaglandin uptake transporter PGT, which indicated that iPGE2 contributes to hypoxia-induced apoptosis (on the contrary, hypoxia/reoxygenation-induced PTC death was exclusively due to extracellular PGE2). Thus, iPGE2 is a new actor in the pathogenesis of hypoxia-induced tubular injury and PGT might be a new therapeutic target for the prevention of hypoxia-dependent lesions in renal diseases.
Smooth transportation of liquid metal droplets in a microchannel as detected by a serially arranged capacitive device
Authors: Konishi Satoshi , Kakehi Yugo , Mori Fuminari , Bono Shinji 
Published: March 2021

AbstractGallium alloy liquid metals (Galinstan) possessing fluidity, electric conductivity, and low toxicity are attractive for use in flexible devices and microfluidic devices. However, the oxide skin of Galinstan in the atmosphere adheres to the microchannel surface, preventing the transportation of Galinstan in the channel. To tackle the problem of the adhesion of Galinstan to microchannel, we introduced liquid with Galinstan into a channel with a diameter of 1000 μm. Then, we found that the cylindrical shape of the channel enabled smooth transportation of Galinstan independently of both the liquid and the channel material. The liquid introduced with Galinstan not only prevents adhesion but also improves the spatial controllability of Galinstan in the channel. We can control the position of Galinstan with 100 μm resolution using highly viscous (> 10 cSt) liquid. In addition, we combined the microchannel with patterned electrodes, fabricating a serially arranged capacitive device. The local capacitance detected by the patterned electrodes changed by more than 6% via the smooth transportation of Galinstan. The analysis results based on an equivalent circuit quantitatively agree with our experimental results. We can modulate the serially arranged capacitors using the smooth transportation of Galinstan in the channel.
Temporal dynamics of intradermal cytokine response to tuberculin in Mycobacterium bovis BCG-vaccinated cattle using sampling microneedles
Authors: Steinbach Sabine , Jalili-Firoozinezhad Sasan , Srinivasan Sreenidhi , Melo Mariane B. , Middleton Sonya , Konold Timm , Coad Michael , Hammond Paula T. , Irvine Darrell J. , Vordermeier Martin , Kapur Vivek 
Published: March 2021

AbstractBovine tuberculosis (bTB) is a disease of livestock with severe and worldwide economic, animal welfare and zoonotic consequences. Application of test-and-slaughter-based control polices reliant on tuberculin skin testing has been the mainstay of bTB control in cattle. However, little is known about the temporal development of the bovine tuberculin skin test response at the dermal sites of antigen injection. To fill this knowledge gap, we applied minimally-invasive sampling microneedles (SMNs) for intradermal sampling of interstitial fluid at the tuberculin skin test sites in Mycobacterium bovis BCG-vaccinated calves and determined the temporal dynamics of a panel of 15 cytokines and chemokines in situ and in the peripheral blood. The results reveal an orchestrated and coordinated cytokine and local chemokine response, identified IL-1RA as a potential soluble biomarker of a positive tuberculin skin response, and confirmed the utility of IFN-γ and IP-10 for bTB detection in blood-based assays. Together, the results highlight the utility of SMNs to identify novel biomarkers and provide mechanistic insights on the intradermal cytokine and chemokine responses associated with the tuberculin skin test in BCG-sensitized cattle.
The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
Authors: Faddetta Teresa , Abbate Loredana , Alibrandi Pasquale , Arancio Walter , Siino Davide , Strati Francesco , De Filippo Carlotta , Fatta Del Bosco Sergio , Carimi Francesco , Puglia Anna Maria , Cardinale Massimiliano , Gallo Giuseppe , Mercati Francesco 
Published: March 2021

AbstractCitrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.
Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases
Authors: Cross Emily M. , Adams Felise G. , Waters Jack K. , Aragão David , Eijkelkamp Bart A. , Forwood Jade K. 
Published: March 2021

AbstractTreatments for ‘superbug’ infections are the focus for innovative research, as drug resistance threatens human health and medical practices globally. In particular, Acinetobacter baumannii (Ab) infections are repeatedly reported as difficult to treat due to increasing antibiotic resistance. Therefore, there is increasing need to identify novel targets in the development of different antimicrobials. Of particular interest is fatty acid synthesis, vital for the formation of phospholipids, lipopolysaccharides/lipooligosaccharides, and lipoproteins of Gram-negative envelopes. The bacterial type II fatty acid synthesis (FASII) pathway is an attractive target for the development of inhibitors and is particularly favourable due to the differences from mammalian type I fatty acid synthesis. Discrete enzymes in this pathway include two reductase enzymes: 3-oxoacyl-acyl carrier protein (ACP) reductase (FabG) and enoyl-ACP reductase (FabI). Here, we investigate annotated FabG homologs, finding a low-molecular weight 3-oxoacyl-ACP reductase, as the most likely FASII FabG candidate, and high-molecular weight 3-oxoacyl-ACP reductase (HMwFabG), showing differences in structure and coenzyme preference. To date, this is the second bacterial high-molecular weight FabG structurally characterized, following FabG4 from Mycobacterium. We show that ΔAbHMwfabG is impaired for growth in nutrient rich media and pellicle formation. We also modelled a third 3-oxoacyl-ACP reductase, which we annotated as AbSDR. Despite containing residues for catalysis and the ACP coordinating motif, biochemical analyses showed limited activity against an acetoacetyl-CoA substrate in vitro. Inhibitors designed to target FabG proteins and thus prevent fatty acid synthesis may provide a platform for use against multidrug-resistant pathogens including A. baumannii.
Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)
Authors: Lupo Giuseppe Francesco Damiano , Rocchetti Gabriele , Lucini Luigi , Lorusso Lorenzo , Manara Elena , Bertelli Matteo , Puglisi Edoardo , Capelli Enrica 
Published: March 2021

AbstractChronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) is a severe multisystemic disease characterized by immunological abnormalities and dysfunction of energy metabolism. Recent evidences suggest strong correlations between dysbiosis and pathological condition. The present research explored the composition of the intestinal and oral microbiota in CFS/ME patients as compared to healthy controls. The fecal metabolomic profile of a subgroup of CFS/ME patients was also compared with the one of healthy controls. The fecal and salivary bacterial composition in CFS/ME patients was investigated by Illumina sequencing of 16S rRNA gene amplicons. The metabolomic analysis was performed by an UHPLC-MS. The fecal microbiota of CFS/ME patients showed a reduction of Lachnospiraceae, particularly Anaerostipes, and an increased abundance of genera Bacteroides and Phascolarctobacterium compared to the non-CFS/ME groups. The oral microbiota of CFS/ME patients showed an increase of Rothia dentocariosa. The fecal metabolomic profile of CFS/ME patients revealed high levels of glutamic acid and argininosuccinic acid, together with a decrease of alpha-tocopherol. Our results reveal microbial signatures of dysbiosis in the intestinal microbiota of CFS/ME patients. Further studies are needed to better understand if the microbial composition changes are cause or consequence of the onset of CFS/ME and if they are related to any of the several secondary symptoms.
Bilingualism is a long-term cognitively challenging experience that modulates metabolite concentrations in the healthy brain
Authors: Pliatsikas Christos , Pereira Soares S. M. , Voits T. , Deluca V. , Rothman J. 
Published: March 2021

AbstractCognitively demanding experiences, including complex skill acquisition and processing, have been shown to induce brain adaptations, at least at the macroscopic level, e.g. on brain volume and/or functional connectivity. However, the neurobiological bases of these adaptations, including at the cellular level, are unclear and understudied. Here we use bilingualism as a case study to investigate the metabolic correlates of experience-based brain adaptations. We employ Magnetic Resonance Spectroscopy to measure metabolite concentrations in the basal ganglia, a region critical to language control which is reshaped by bilingualism. Our results show increased myo-Inositol and decreasedN-acetyl aspartate concentrations in bilinguals compared to monolinguals. Both metabolites are linked to synaptic pruning, a process underlying experience-based brain restructuring. Interestingly, both concentrations correlate with relative amount of bilingual engagement. This suggests that degree of long-term cognitive experiences matters at the level of metabolic concentrations, which might accompany, if not drive, macroscopic brain adaptations.
Developing a medium combination to attain similar glycosylation profile to originator by DoE and cluster analysis method
Authors: Xu Jian , Shao Zhihui , Wang Zhanqing , Huang Yingfeng , Zou Xun , Shen Yaling 
Published: March 2021

AbstractGlycosylation is critical for monoclonal antibody production because of its impact on pharmacokinetics and pharmacodynamics. Modulation of glycan profile is frequently needed in biosimilar development. However, glycosylation profile is not a single value like that of cell culture titer, hence making it challenging for the Design of Experiment (DoE) methodology to be directly applied. In this study, a Her2-binding antibody was developed as a biosimilar to Herceptin. Cluster analysis was introduced to demonstrate the similarity of glycan profiles between the samples and the reference with specific value—distance. The glycosylation was subsequently optimized with the DoE method. Basal medium and feed medium were found to be the significant factors to the glycosylation pattern. Moreover, a combination of medium and feed strategy was developed to attain the most similar glycoprotein molecule to that of the originator biologic drug. This study may provide an additional option to evaluate multivariable factors and assess biosimilarity and/or comparability in monoclonal antibody production.
Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies
Authors: Laserna-Mendieta E. J. , FitzGerald J. A. , Arias-Gonzalez L. , Ollala J. M. , Bernardo D. , Claesson M. J. , Lucendo A. J. 
Published: March 2021

AbstractEosinophilic esophagitis (EoE) is a chronic, immune-mediated inflammatory esophageal disease triggered by food antigens. Cumulative evidence supports the implication of microbiota and the innate immune system in the pathogenesis of EoE. Changes in the esophageal microbiome were investigated by applying 16S rRNA gene sequencing on esophageal biopsies of adult patients with active EoE at baseline (n = 30), and after achieving remission with either proton pump inhibitors (PPI, n = 10), swallowed topical corticosteroids (STC, n = 10) or food-elimination diets (FED, n = 10). Ten non-EoE biopsies were also characterized as controls. Compared to controls, no differences in alpha (intra-sample) diversity were found in EoE microbiota overall. However, it decreased significantly among patients who underwent FED. As for beta (inter-sample) diversity, non-EoE controls separated from EoE baseline samples. Post-treatment samples from patients treated with PPI and FED had a more similar microbiota composition, while those receiving STC were closer to controls. Differential testing of microbial relative abundance displayed significant changes for Filifactor, Parvimonas and Porphyromonas genera. Analysis of predicted functions indicated alterations in metabolic pathways and abundance of sulphur-cytochrome oxidoreductases. Our findings demonstrate changes in microbiota associated with EoE, as well as a treatment effect on the microbiome.
Influence of soil heterogeneity on soybean plant development and crop yield evaluated using time-series of UAV and ground-based geophysical imagery
Authors: Falco Nicola , Wainwright Haruko M. , Dafflon Baptiste , Ulrich Craig , Soom Florian , Peterson John E. , Brown James Bentley , Schaettle Karl B. , Williamson Malcolm , Cothren Jackson D. , Ham Richard G. , McEntire Jay A. , Hubbard Susan S. 
Published: March 2021

AbstractUnderstanding the interactions among agricultural processes, soil, and plants is necessary for optimizing crop yield and productivity. This study focuses on developing effective monitoring and analysis methodologies that estimate key soil and plant properties. These methodologies include data acquisition and processing approaches that use unmanned aerial vehicles (UAVs) and surface geophysical techniques. In particular, we applied these approaches to a soybean farm in Arkansas to characterize the soil–plant coupled spatial and temporal heterogeneity, as well as to identify key environmental factors that influence plant growth and yield. UAV-based multitemporal acquisition of high-resolution RGB (red–green–blue) imagery and direct measurements were used to monitor plant height and photosynthetic activity. We present an algorithm that efficiently exploits the high-resolution UAV images to estimate plant spatial abundance and plant vigor throughout the growing season. Such plant characterization is extremely important for the identification of anomalous areas, providing easily interpretable information that can be used to guide near-real-time farming decisions. Additionally, high-resolution multitemporal surface geophysical measurements of apparent soil electrical conductivity were used to estimate the spatial heterogeneity of soil texture. By integrating the multiscale multitype soil and plant datasets, we identified the spatiotemporal co-variance between soil properties and plant development and yield. Our novel approach for early season monitoring of plant spatial abundance identified areas of low productivity controlled by soil clay content, while temporal analysis of geophysical data showed the impact of soil moisture and irrigation practice (controlled by topography) on plant dynamics. Our study demonstrates the effective coupling of UAV data products with geophysical data to extract critical information for farm management.
The gut microbiota metabolite urolithin A inhibits NF-κB activation in LPS stimulated BMDMs
Authors: Abdelazeem Khalid N. M. , Kalo M. Zaher , Beer-Hammer Sandra , Lang Florian 
Published: March 2021

AbstractInflammation is a natural defense process of the innate immune system, associated with the release of proinflammatory cytokines such as interleukin-1β, interleukin-6, interleukin-12 and TNFα; and enzymes including iNOS through the activation and nuclear translocation of NF-κB p65 due to the phosphorylation of IκBα. Regulation of intracellular Ca2+ is considered a promising strategy for the prevention of reactive oxygen species (ROS) production and accumulation of DNA double strand breaks (DSBs) that occurs in inflammatory-associated-diseases. Among the metabolites of ellagitannins that are produced in the gut microbiome, urolithin A (UA) has received an increasing attention as a novel candidate with anti-inflammatory and anti-oxidant effects. Here, we investigated the effect of UA on the suppression of pro-inflammatory molecules and NF-κB activation by targeting TLR4 signalling pathway. We also identified the influence of UA on Ca2+ entry, ROS production and DSBs availability in murine bone-marrow-derived macrophages challenged with lipopolysaccharides (LPS). We found that UA inhibits IκBα phosphorylation and supresses MAPK and PI3K activation. In addition, UA was able to reduce calcium entry, ROS production and DSBs availability. In conclusion, we suggest that urolithin A is a promising therapeutic agent for treating inflammatory diseases through suppression of NF-κB and preserving DNA through maintaining intracellular calcium and ROS homeostasis.
Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study
Authors: Mishra Binisha H. , Mishra Pashupati P. , Raitoharju Emma , Marttila Saara , Mononen Nina , Sievänen Harri , Viikari Jorma , Juonala Markus , Laaksonen Marika , Hutri-Kähönen Nina , Kähönen Mika , Raitakari Olli T. , Lehtimäki Terho 
Published: March 2021

AbstractWe analysed whole blood genome-wide expression data to identify gene co-expression modules shared by early traits of osteoporosis and atherosclerosis. Gene expression was profiled for the Young Finns Study participants. Bone mineral density and content were measured as early traits of osteoporosis. Carotid and bulbus intima media thickness were measured as early traits of atherosclerosis. Joint association of the modules, identified with weighted co-expression analysis, with early traits of the diseases was tested with multivariate analysis. Among the six modules significantly correlated with early traits of both the diseases, two had significant (adjusted p-values (p.adj) < 0.05) and another two had suggestively significant (p.adj < 0.25) joint association with the two diseases after adjusting for age, sex, body mass index, smoking habit, alcohol consumption, and physical activity. The three most significant member genes from the significant modules were NOSIP, GXYLT2, and TRIM63 (p.adj ≤ 0.18). Genes in the modules were enriched with biological processes that have separately been found to be involved in either bone metabolism or atherosclerosis. The gene modules and their most significant member genes identified in this study support the osteoporosis-atherosclerosis comorbidity hypothesis and can provide new joint biomarkers for both diseases and their dual prevention.
A prostate-specific membrane antigen (PSMA)-targeted prodrug with a favorable in vivo toxicity profile
Authors: Boinapally Srikanth , Ahn Hye-Hyun , Cheng Bei , Brummet Mary , Nam Hwanhee , Gabrielson Kathleen L. , Banerjee Sangeeta R. , Minn Il , Pomper Martin G. 
Published: March 2021

AbstractProstate-specific membrane antigen (PSMA) is a promising target for the treatment of advanced prostate cancer (PC) and various solid tumors. Although PSMA-targeted radiopharmaceutical therapy (RPT) has enabled significant imaging and prostate-specific antigen (PSA) responses, accumulating clinical data are beginning to reveal certain limitations, including a subgroup of non-responders, relapse, radiation-induced toxicity, and the need for specialized facilities for its administration. To date non-radioactive attempts to leverage PSMA to treat PC with antibodies, nanomedicines or cell-based therapies have met with modest success. We developed a non-radioactive prodrug, SBPD-1, composed of a small-molecule PSMA-targeting moiety, a cancer-selective cleavable linker, and the microtubule inhibitor monomethyl auristatin E (MMAE). SBPD-1 demonstrated high binding affinity to PSMA (Ki = 8.84 nM) and selective cytotoxicity to PSMA-expressing PC cell lines (IC50 = 3.90 nM). SBPD-1 demonstrated a significant survival benefit in two murine models of human PC relative to controls. The highest dose tested did not induce toxicity in immunocompetent mice. The high specific targeting ability of SBPD-1 to PSMA-expressing tumors and its favorable toxicity profile warrant its further development.
Biochemical and structural characterization of analogs of MRE11 breast cancer-associated mutant F237C
Authors: Rahman Samiur , Beikzadeh Mahtab , Latham Michael P. 
Published: March 2021

AbstractThe MRE11–RAD50–NBS1 (MRN) protein complex plays a vital role in DNA double strand break sensing, signaling, and repair. Mutation in any component of this complex may lead to disease as disrupting DNA double strand break repair has the potential to cause translocations and loss of genomic information. Here, we have investigated an MRE11 mutation, F237C, identified in a breast cancer tumor. We found that the analogous mutant of Pyrococcus furiosus Mre11 diminishes both the exonuclease and endonuclease activities of Mre11 in vitro. Solution state NMR experiments show that this mutant causes structural changes in the DNA-bound Mre11 for both exo- and endonuclease substrates and causes the protein to become generally more rigid. Moreover, by comparing the NMR data for this cancer-associated mutant with two previously described Mre11 separation-of-nuclease function mutants, a potential allosteric network was detected within Mre11 that connects the active site to regions responsible for recognizing the DNA ends and for dimerization. Together, our data further highlight the dynamics required for Mre11 nuclease function and illuminate the presence of allostery within the enzyme.