bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis links alterations of bioenergetics, mitochondria-ER interactions and proteostasis in hippocampal astrocytes from 3xTg-AD mice
Authors: Dematteis Giulia , Vydmantaitė Gabrielė , Ruffinatti Federico Alessandro , Chahin Malak , Farruggio Serena , Barberis Elettra , Ferrari Eleonora , Marengo Emilio , Distasi Carla , Morkūnienė Ramunė , Genazzani Armando A. , Grilli Mariagrazia , Grossini Elena , Corazzari Marco , Manfredi Marcello , Lim Dmitry , Jekabsone Aistė , Tapella Laura 
Published: August 2020

AbstractThe pathogenesis of Alzheimer’s disease (AD), a slowly-developing age-related neurodegenerative disorder, is a result of the action of multiple factors including deregulation of Ca2+ homeostasis, mitochondrial dysfunction, and dysproteostasis. Interaction of these factors in astrocytes, principal homeostatic cells in the central nervous system, is still poorly understood. Here we report that in immortalized hippocampal astrocytes from 3xTg-AD mice (3Tg-iAstro cells) bioenergetics is impaired, including reduced glycolysis and mitochondrial oxygen consumption, and increased production of reactive oxygen species. Shotgun proteomics analysis of mitochondria-ER-enriched fraction showed no alterations in the expression of mitochondrial and OxPhos proteins, while those related to the ER functions and protein synthesis were deregulated. Using ER- and mitochondria-targeted aequorin-based Ca2+ probe we show that, in 3Tg-iAstro cells, ER was overloaded with Ca2+ while Ca2+ uptake by mitochondria upon ATP stimulation was reduced. This was accompanied by the increase in short distance (≈8–10 nm) contact area between mitochondria and ER, upregulation of ER-stress/unfolded protein response genes Atf4, Atf6 and Herp, and reduction of global protein synthesis rate. We suggest that familial AD mutations in 3Tg-iAstro cells induce mitochondria-ER interaction changes that deregulate astrocytic bioenergetics, Ca2+ homeostasis and proteostasis. These factors may interact, creating a pathogenic loop compromising homeostatic and defensive functions of astroglial cells predisposing neurons to dysfunction.
Key role of quinone in the mechanism of respiratory complex I
Authors: Gutiérrez-Fernández Javier , Kaszuba Karol , Minhas Gurdeep S. , Baradaran Rozbeh , Tambalo Margherita , Gallagher David T. , Sazanov Leonid A. 
Published: August 2020

AbstractComplex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
Interaction of the pioneer transcription factor GATA3 with nucleosomes
Authors: Tanaka Hiroki , Takizawa Yoshimasa , Takaku Motoki , Kato Daiki , Kumagawa Yusuke , Grimm Sara A. , Wade Paul A. , Kurumizaka Hitoshi 
Published: August 2020

AbstractDuring cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation. Here, we use high-resolution nucleosome mapping in human cells to explore the impact of the position of GATA motifs on the surface of nucleosomes on productive enhancer formation, finding productivity correlates with binding sites located near the nucleosomal dyad axis. Biochemical experiments with model nucleosomes demonstrate sufficiently stable transcription factor-nucleosome interaction to empower cryo-electron microscopy structure determination of the complex at 3.15 Å resolution. The GATA3 zinc fingers efficiently bind their target 5′-GAT-3′ sequences in the nucleosome when they are located in solvent accessible, consecutive major grooves without significant changes in nucleosome structure. Analysis of genomic loci bound by GATA3 during reprogramming suggests a correlation of recognition motif sequence and spacing that may distinguish productivity of new enhancer formation.
Chemical synthesis of glycans up to a 128-mer relevant to the O-antigen of Bacteroides vulgatus
Authors: Zhu Qian , Shen Zhengnan , Chiodo Fabrizio , Nicolardi Simone , Molinaro Antonio , Silipo Alba , Yu Biao 
Published: August 2020

AbstractGlycans are involved in various life processes and represent critical targets of biomedical developments. Nevertheless, the accessibility to long glycans with precise structures remains challenging. Here we report on the synthesis of glycans consisting of [→4)-α-Rha-(1 → 3)-β-Man-(1 → ] repeating unit, which are relevant to the O-antigen of Bacteroides vulgatus, a common component of gut microbiota. The optimal combination of assembly strategy, protecting group arrangement, and glycosylation reaction has enabled us to synthesize up to a 128-mer glycan. The synthetic glycans are accurately characterized by advanced NMR and MS approaches, the 3D structures are defined, and their potent binding activity with human DC-SIGN, a receptor associated with the gut lymphoid tissue, is disclosed.
Lipoarabinomannan antigenic epitope differences in tuberculosis disease subtypes
Authors: Magni Ruben , Rruga Fatlum , Alsaab Fahad M. , Sharif Sara , Howard Marissa , Espina Virginia , Kim Brianna , Lepene Benjamin , Lee Gwenyth , Alayouni Mohamad A. , Steinberg Hannah , Araujo Robyn , Kashanchi Fatah , Riccardi Fabio , Morreira Sargento , Araujo Antonia , Poli Fernando , Jaganath Devan , Semitala Fred C. , Worodria William , Andama Alfred , Choudhary Alok , Honnen William J. , Petricoin Emanuel F. , Cattamanchi Adithya , Colombatti Raffaella , de Waard Jacobus H. , Oberhelman Richard , Pinter Abraham , Gilman Robert H. , Liotta Lance A. , Luchini Alessandra 
Published: August 2020

AbstractAn accurate urine test for diverse populations with active tuberculosis could be transformative for preventing TB deaths. Urinary liporabinomannan (LAM) testing has been previously restricted to HIV co-infected TB patients. In this study we evaluate urinary LAM in HIV negative, pediatric and adult, pulmonary and extrapulmonary tuberculosis patients. We measured 430 microbiologically confirmed pretreatment tuberculosis patients and controls from Peru, Guinea Bissau, Venezuela, Uganda and the United States using three monoclonal antibodies, MoAb1, CS35, and A194, which recognize distinct LAM epitopes, a one-sided immunoassay, and blinded cohorts. We evaluated sources of assay variability and comorbidities (HIV and diabetes). All antibodies successfully discriminated TB positive from TB negative patients. ROAUC from the average of three antibodies’ responses was 0.90; 95% CI 0.87–0.93, 90% sensitivity, 73.5% specificity (80 pg/mL). MoAb1, recognizing the 5-methylthio-d-xylofuranose(MTX)-mannose(Man) cap epitope, performed the best, was less influenced by glycosuria and identified culture positive pediatric (N = 19) and extrapulmonary (N = 24) patients with high accuracy (ROAUC 0.87, 95% CI 0.77–0.98, 0.90 sensitivity 0.80 specificity at 80 pg/mL; ROAUC = 0.96, 95% CI 0.92–0.99, 96% sensitivity, 80% specificity at 82 pg/mL, respectively). The MoAb1 antibody, recognizing the MTX-Man cap epitope, is a novel analyte for active TB detection in pediatric and extrapulmonary disease.
Coupling of electrochemical–temperature–mechanical processes in marine clay during electro-osmotic consolidation
Authors: Xue Zhi-Jia , Yan Chang-Gen , Li Wu-Gang 
Published: August 2020

AbstractElectro-osmotic consolidation has been applied in several geotechnical engineering applications that contain a series of complex processes, including electrochemical processes, temperature changes, and mechanical evolution. To explore the combination of electrochemical–temperature–mechanical processes in marine clay, electro-osmotic consolidation experiments were conducted using a self-made electro-osmotic consolidation system under various durations and voltages. The following findings was obtained: (1) the change in the pH value increased during electro-osmotic consolidation and as the voltage rise; (2) the temperature increased with a rise in voltage in the initial stage of the experiments, which was induced by Joule heating; (3) the temperature rise promoted the electro-osmotic consolidation process, which included a rise in the coefficient of consolidation and a reduction in water content; (4) horizontal shrinkage occurred when the horizontal stress increment was greater than the critical stress condition. In addition, the volume difference reached a constant value, and was proportional to the voltage rise. After the discussion, a coupling analysis was conducted, which can help to better understand the mechanism of electro-osmotic consolidation and can provide reference for engineering applications.
Improved host-plant resistance to Phytophthora rot and powdery mildew in soybean (Glycine max (L.) Merr.)
Authors: Ramalingam Jegadeesan , Alagarasan Ganesh , Savitha Palanisamy , Lydia Kelsey , Pothiraj Govindan , Vijayakumar Eswaramoorthy , Sudhagar Rajaprakasam , Singh Amar , Vedna Kumari , Vanniarajan Chockalingam 
Published: August 2020

AbstractSoybean is an important oilseed cum vegetable crop, susceptible to various biotic stresses which is attributed to recent decline in crop productivity. The emergence of virulent biotypes/strains of different plant pathogens necessitates the development of new crop varieties with enhanced host resistance mechanisms. Pyramiding of multiple disease-resistant genes is one of the strategies employed to develop durable disease-resistant cultivars to the prevailing and emerging biotypes of pathogens. The present study, reports the successful introgression of two major R-genes, including Rps2 (Phytophthora rot resistance), Rmd-c (complete-powdery mildew resistance) and effective nodulating gene (rj2) through functional Marker-Assisted Backcross Breeding (MABB) in the genetic background of well-adapted and high yielding soybean varieties, CO 3 and JS 335. We have identified several promising introgressed lines with enhanced resistance to Phytophthora rot and powdery mildew. The improved soybean lines have exhibited medium to high level of resistance against powdery mildew and Phytophthora rot as well as displayed effective nodulation capacity. Our study has proven the generation of resistant genotypes to realize the potential of MABB for achieving host plant resistance in soybean. The improved lines developed can greatly assist the soybean breeding programs in India and other soybean growing countries for evolving disease-resistant varieties.
Targeting cPLA2 derived lipid hydroperoxides as a potential intervention for sarcopenia
Authors: Pharaoh Gavin , Brown Jacob L. , Sataranatarajan Kavithalakshmi , Kneis Parker , Bian Jan , Ranjit Rojina , Hadad Niran , Georgescu Constantin , Rabinovitch Peter , Ran Qitao , Wren Jonathan D. , Freeman Willard , Kinter Michael , Richardson Arlan , Van Remmen Holly 
Published: August 2020

AbstractDefects in neuromuscular innervation contribute significantly to the age-related decline in muscle mass and function (sarcopenia). Our previous studies demonstrated that denervation induces muscle mitochondrial hydroperoxide production (H2O2 and lipid hydroperoxides (LOOHs)). Here we define the relative contribution of mitochondrial electron transport chain (ETC) derived H2O2 versus cytosolic phospholipase A2 (cPLA2) derived LOOHs in neurogenic muscle atrophy. We show that denervation increases muscle cPLA2 protein content, activity, and metabolites downstream of cPLA2 including LOOHs. Increased scavenging of mitochondrial H2O2 does not protect against denervation atrophy, suggesting ETC generated H2O2 is not a critical player. In contrast, inhibition of cPLA2 in vivo mitigates LOOH production and muscle atrophy and maintains individual muscle fiber size while decreasing oxidative damage. Overall, we show that loss of innervation in several muscle atrophy models including aging induces generation of LOOHs produced by arachidonic acid metabolism in the cPLA2 pathway contributing to loss of muscle mass.
Visual motion information modulates tactile roughness perception
Authors: Suzuishi Yosuke , Hidaka Souta , Kuroki Scinob 
Published: August 2020

AbstractWe perceive the roughness of an object through our eyes and hands. Many crossmodal studies have reported that there is no clear visuo-tactile interaction in roughness perception using static visual cues. One exception is that the visual observation of task-irrelevant hand movements, not the texture of task-relevant objects, can enhance the performance of tactile roughness discrimination. Our study investigated whether task-irrelevant visual motion without either object roughness or bodily cues can influence tactile roughness perception. Participants were asked to touch abrasive papers while moving their hand laterally and viewing moving or static sine wave gratings without being able to see their hand, and to estimate the roughness magnitude of the tactile stimuli. Moving gratings with a low spatial frequency induced smoother roughness perceptions than static visual stimuli when the visual grating moved in the direction opposite the hand movements. The effects of visual motion did not appear when the visual stimuli had a high spatial frequency or when the participants touched the tactile stimuli passively. These results indicate that simple task-irrelevant visual movement without object roughness or bodily cues can modulate tactile roughness perception with active body movements in a spatial-frequency-selective manner.
N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont
Authors: Zilius Mindaugas , Bonaglia Stefano , Broman Elias , Chiozzini Vitor Gonsalez , Samuiloviene Aurelija , Nascimento Francisco J. A. , Cardini Ulisse , Bartoli Marco 
Published: August 2020

AbstractMangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.
De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing
Authors: Bertel-Sevilla Angela , Alzate Juan F. , Olivero-Verbel Jesus 
Published: August 2020

AbstractMugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KEGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.
Microseismic records classification using capsule network with limited training samples in underground mining
Authors: Peng Pingan , He Zhengxiang , Wang Liguan , Jiang Yuanjian 
Published: August 2020

AbstractThe identification of suspicious microseismic events is the first crucial step in microseismic data processing. Existing automatic classification methods are based on the training of a large data set, which is challenging to apply in mines without a long-term manual data processing. In this paper, we present a method to automatically classify microseismic records with limited samples in underground mines based on capsule networks (CapsNet). We divide each microseismic record into 33 frames, then extract 21 commonly used features in time and frequency from each frame. Consequently, a 21 × 33 feature matrix is utilized as the input of CapsNet. On this basis, we use different sizes of training sets to train the classification models separately. The trained model is tested using the same test set containing 3,200 microseismic records and compared to convolutional neural networks (CNN) and traditional machine learning methods. Results show that the accuracy of our proposed method is 99.2% with limited training samples. It is superior to CNN and traditional machine learning methods in terms of Accuracy, Precision, Recall, F1-Measure, and reliability.
Sitting-induced hemodynamic changes and association with sitting intolerance in children and adolescents: a cross-sectional study
Authors: Tao Chunyan , Han Zhenhui , Yan Yongqiang , Pan Zhitao , Zhu Hanwen , Li Xueying , Li Hongxia , Wang Yuanyuan , Liu Ping , Wang Yuli , Jiang Min , Tang Chaoshu , Jin Hongfang , Du Junbao 
Published: August 2020

AbstractHemodynamic alteration with postural change from supine to sitting has been unclear in the young. In the cross-sectional study, 686 participants (371 boys and 315 girls, aged 6–18 years) were recruited from 4 schools in Kaifeng city, the central area of China. The active sitting test was performed to obtain heart rate (HR) and blood pressure (BP) changes from supine to sitting in children and adolescents. Hemodynamic change-associated sitting intolerance was analyzed. In the study participants, the 95th percentile (P95) values of changes in HR and BP within 3 min from supine to sitting were 25 beats/min and 18/19 mm Hg, respectively. Sixty-six participants had sitting intolerance symptoms. Compared with participants without sitting intolerance symptoms, those with symptoms more frequently had HR increase ≥ P95 or BP increase ≥ P95 within 3 min from supine to sitting (P < 0.001). Risk factors for sitting intolerance were age (odds ratio 1.218, 95% confidence interval 1.072–1.384, P = 0.002) and changes in HR or BP ≥ P95 within 3 min after sitting (odds ratio 2.902, 95% confidence interval 1.572–5.357, P = 0.001). We firstly showed hemodynamic changing profiles from supine to sitting and their association with sitting intolerance in children and adolescents. Sitting tachycardia is likely suggested with a change in HR ≥ 25 beats/min and sitting hypertension with a change in BP ≥ 20/20 mm Hg when changing from supine to sitting within 3 min. The age and changes in HR or BP were independent risk factors for sitting intolerance.
Characterization of immune response induced against catalytic domain of botulinum neurotoxin type E
Authors: Sonkar Priyanka , Chauhan Vinita , Chauhan Ritika , Saxena Nandita , Dhaked Ram Kumar 
Published: August 2020

AbstractBotulinum neurotoxins (BoNTs) represent a family of bacterial toxins responsible for neuroparalytic disease ‘botulism’ in human and animals. Their potential use as biological weapon led to their classification in category ‘A’ biowarfare agent by Centers for Disease Control and Prevention (CDC), USA. In present study, gene encoding full length catalytic domain of BoNT/E-LC was cloned, expressed and protein was purified using Ni–NTA chromatography. Humoral immune response was confirmed by Ig isotyping and cell-mediated immunity by cytokine profiling and intracellular staining for enumeration of IFN-γ secreting CD4+ and CD8+ T cells. Increased antibody titer with the predominance of IgG subtype was observed. An interaction between antibodies produced against rBoNT/E-LC was established that showed the specificity against BoNT/E in SPR assay. Animal protection with rBoNT/E-LC was conferred through both humoral and cellular immune responses. These findings were supported by cytokine profiling and flow cytometric analysis. Splenocytes stimulated with rBoNT/E-LC showed a 3.27 and 2.8 times increase in the IFN-γ secreting CD4+ and CD8+ T cells, respectively; in immunized group (P < 0.05). Protection against BoNT/E challenge tended to relate with increase in the percentage of rBoNT/E-LC specific IL-2 in the splenocytes supernatant (P = 0.034) and with IFN-γ-producing CD4+ T cell responses (P = 0.045). We have immunologically evaluated catalytically active rBoNT/E-LC. Our results provide valuable investigational report for immunoprophylactic role of catalytic domain of BoNT/E.