bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chlamydomonas reinhardtii exhibits stress memory in the accumulation of triacylglycerols induced by nitrogen deprivation
Authors: Mikulski Pawel , Santos-Aberturas Javier 
Published: July 2021

SummaryStress memory is a phenomenon whereby exposure to initial stress event influences a response to subsequent stress exposures. Studying stress memory is important to understand the cellular behaviour in dynamic environment, especially nowadays, in times with growing environmental instability. Stress memory has been characterized in vascular plants but its occurrence in non-vascular plant species has been rarely investigated.We hypothesized that stress memory occurs in non-vascular plants in relation to metabolic stress. We sought to test it using accumulation of lipids (triacylglycerols) in model green alga Chlamydomonas reinhardtii subjected to nitrogen deprivation stress as a model system.Here, we established stress memory protocol on C. reinhardtii cells. Using a blend of microscopy and gas chromatography methods, we showed that the cells exposed to recurrent stress show differential accumulation of triacylglycerols on the quantitative level without qualitative changes in lipid composition, comparing to single stress controls.Overall, our results suggest that metabolic stress memory does occur in non-vascular plant C. reinhardtii and provides a starting point to characterize metabolic stress memory mechanism. Due to the commercial potential of algae, our findings are relevant for basic science, as well as industrial production of algae-derived compounds.
Thein vitroandin vivopotency of CT-P59 against Delta and its associated variants of SARS-CoV-2
Authors: Ryu Dong-Kyun , Woo Hye-Min , Kang Bobin , Noh Hanmi , Kim Jong-In , Seo Ji-Min , Kim Cheolmin , Kim Minsoo , Kim Jun-Won , Kim Nayoung , Jeon Pyeonghwa , Lee Hansaem , Yang Jeong-Sun , Kim Kyung-Chang , Lee Joo-Yeon , Lee Min-Ho , Oh Sang-Seok , Chung Hyo-Young , Kwon Ki-Sung , Lee Soo-Young 
Published: July 2021

AbstractThe Delta variant originally from India is rapidly spreading across the world and causes to resurge infections of SARS-CoV-2. We previously reported that CT-P59 presented itsin vivopotency against Beta and Gamma variants, despite its reduced activity in cell experiments. Yet, it remains uncertain to exert the antiviral effect of CT-P59 on the Delta and its associated variants (L452R). To tackle this question, we carried out cell tests and animal study. CT-P59 showed reduced antiviral activity but enabled neutralization against Delta, Epsilon, and Kappa variants in cells. In line within vitroresults, the mouse challenge experiment with the Delta variant substantiatedin vivopotency of CT-P59 showing symptom remission and virus abrogation in the respiratory tract. Collectively, cell and animal studies showed that CT-P59 is effective against the Delta variant infection, hinting that CT-P59 has therapeutic potency for patients infected with Delta and its associated variants.HighlightsCT-P59 exerts the antiviral effect on authentic Delta, Epsilon and Kappa variants in cell-based experiments.CT-P59 showed neutralizing potency against variants including Delta, Epsilon, Kappa, L452R, T478K and P681H pseudovirus variants.The administration of clinically relevant dose of CT-P59 showedin vivoprotection against Delta variants in animal challenge experiment.
Phage Resistance Mechanisms Increase Colistin Sensitivity in Acinetobacter baumannii
Authors: Wang Xiaoqing , Loh Belinda , Yu Yunsong , Hua Xiaoting , Leptihn Sebastian 
Published: July 2021

ABSTRACTFew emergency-use antibiotics remain for the treatment of multidrug-resistant bacterial infections. Infections with resistant bacteria are becoming increasingly common. Phage therapy has reemerged as a promising strategy to treat such infections, as microbial viruses are not affected by bacterial resistance to antimicrobial compounds. However, phage therapy is impeded by rapid emergence of phage-resistant bacteria during therapy. In this work, we studied phage-resistance of colistin sensitive and resistant A. baumannii strains. Using whole genome sequencing, we determined that phage resistant strains displayed mutations in genes that alter the architecture of the bacterial envelope. In contrast to previous studies where phage-escape mutants showed decreased binding of phages to the bacterial envelope, we obtained several not uninfectable isolates that allowed similar phage adsorption compared to the susceptible strain. When phage-resistant bacteria emerged in the absence of antibiotics, we observed that the colistin resistance levels often decreased, while the antibiotic resistance mechanism per se remained unaltered. In particular the two mutated genes that conveyed phage resistance, a putative amylovoran-biosynthesis and a lipo-oligosaccharide (LOS) biosynthesis gene, impact colistin resistance as the mutations increased sensitivity to the antibiotic.
GAN-GMHI: Generative Adversarial Network for high discrimination power in microbiome-based disease prediction
Authors: Li Yuxue , Xie Gang , Zha Yuguo , Ning Kang 
Published: July 2021

AbstractGut microbiome-based health index (GMHI) has been applied with success, while the discrimination powers of GMHI varied for different diseases, limiting its utility on a broad-spectrum of diseases. In this work, a generative adversarial network (GAN) model is proposed to improve the discrimination power of GMHI. Built based on the batch corrected data through GAN, GAN-GMHI has largely reduced the batch effects, and profoundly improved the performance for distinguishing healthy individuals and different diseases. GAN-GMHI has provided a solution to unravel the strong association of gut microbiome and diseases, and indicated a more accurate venue toward microbiome-based disease monitoring. The code for GAN-GMHI is available at https://github.com/HUST-NingKang-Lab/GAN-GMHI.ImportanceThe association of gut microbiome and diseases has been proven for many diseases, while the transformation of such association to a robust and universal disease prediction model has remained illusive, largely due to the batch effects presents in multiple microbiome cohorts. Our analyses have indicated a plausible venue, which is based on GAN technique, towards batch effect removal for microbiome datasets. GAN-GMHI is a novel method built based on the batch corrected data through GAN, as well as GMHI for prediction of a broad-spectrum of diseases.
TMPRSS2 promotes SARS-CoV-2 evasion from NCOA7-mediated restriction
Authors: Khan H , Winstone H , Jimenez-Guardeño J , Graham C , Doores KJ , Goujon C , Matthews DA , Davidson AD , Rihn SJ , Palmarini M , Neil SJD , Malim MH 
Published: July 2021

AbstractInterferons play a critical role in regulating host immune responses to SARS-CoV-2, but the interferon (IFN)-stimulated gene (ISG) effectors that inhibit SARS-CoV-2 are not well characterized. The IFN-inducible short isoform of human nuclear receptor coactivator 7 (NCOA7) inhibits endocytic virus entry, interacts with the vacuolar ATPase, and promotes endo-lysosomal vesicle acidification and lysosomal protease activity. Here, we used ectopic expression and gene knockout to demonstrate that NCOA7 inhibits infection by SARS-CoV-2 as well as by lentivirus particles pseudotyped with SARS-CoV-2 Spike in lung epithelial cells. Infection with the highly pathogenic, SARS-CoV-1 and MERS-CoV, or seasonal, HCoV-229E and HCoV-NL63, coronavirus Spike-pseudotyped viruses was also inhibited by NCOA7. Importantly, either overexpression of TMPRSS2, which promotes plasma membrane fusion versus endosomal fusion of SARS-CoV-2, or removal of Spike’s polybasic furin cleavage site rendered SARS-CoV-2 less sensitive to NCOA7 restriction. Collectively, our data indicate that furin cleavage sensitizes SARS-CoV-2 Spike to the antiviral consequences of endosomal acidification by NCOA7, and suggest that the acquisition of furin cleavage may have favoured the co-option of cell surface TMPRSS proteases as a strategy to evade the suppressive effects of IFN-induced endo-lysosomal dysregulation on virus infection.
DNA-damage induced cell death in yap1;wwtr1 mutant epidermal basal cells
Authors: Lai Jason K. H. , Toh Pearlyn J. Y. , Cognart Hamizah A. , Chouhan Geetika , Saunders Timothy E. 
Published: July 2021

ABSTRACTIn a previous study, it was reported that Yap1 and Wwtr1 in zebrafish regulates the morphogenesis of the posterior body and epidermal fin fold (Kimelman, D., et al. 2017). We report here that DNA damage induces apoptosis of epidermal basal cells (EBCs) in zebrafish yap1−/−;wwtr1−/− embryos. Specifically, these mutant EBCs exhibit active Caspase-3, Caspase-8 and γH2AX, consistent with DNA damage serving as a stimulus of the extrinsic apoptotic pathway in epidermal cells. Live imaging of zebrafish epidermal cells reveals a steady growth of basal cell size in the developing embryo, but this growth is inhibited in mutant basal cells followed by apoptosis, leading to the hypothesis that factors underscoring cell size play a role in this DNA damage-induced apoptosis phenotype. We tested two of these factors using cell stretching and substrate stiffness assays, and found that HaCaT cells cultured on stiff substrates exhibit more numerous γH2AX foci compared to ones cultured on soft substrates. Thus, we propose that substrate rigidity modulates genomic stress in the developing epidermal cell, and that Yap1 and Wwtr1 are required for its survival.
The “neural shift” of sleep quality and cognitive ageing: A resting-state MEG study of transient neural dynamics
Authors: Tibon Roni ,   Cam-CAN, Tsvetanov Kamen A. 
Published: July 2021

AbstractSleep quality changes dramatically from young to old age, but its effects on brain dynamics and cognitive functions are not yet fully specified. We applied Hidden Markov Models (HMMs) to resting-state MEG data from a large cohort (N=564) of population-based adults (aged 18-88), in order to characterize transient neural networks and to relate their temporal dynamics to sleep quality and to cognitive performance. Using multivariate analyses of brain-sleep profiles and of brain-cognition profiles, we found that an age-related “neural shift”, expressed as decreased occurrence of “lower-order” brain networks, coupled with increased occurrence of “higher-order” networks, was associated with both increased sleep dysfunction and decreased fluid intelligence above and beyond age. These results suggest that poor sleep quality, as evident in ageing, may lead to a behavior-related shift in neural dynamics.
Shifts in leaf senescence across the Northern Hemisphere in response to seasonal warming
Authors: Chen Lei , Rossi Sergio , Smith Nicholas G. , Liu Jianquan 
Published: July 2021

SummaryShifts in plant phenology under ongoing warming affect global vegetation dynamics and carbon assimilation of the biomes. The response of leaf senescence to climate is crucial for predicting changes in the physiological processes of trees at ecosystem scale. We used long-term ground observations, phenological metrics derived from PhenoCam, and satellite imagery of the Northern Hemisphere to show that the timings of leaf senescence can advance or delay in case of warming occurring at the beginning (before June) or during (after June) the main growing season, respectively. Flux data demonstrated that net photosynthetic carbon assimilation converted from positive to negative at the end of June. These findings suggest that leaf senescence is driven by carbon assimilation and nutrient resorption at different growth stages of leaves. Our results provide new insights into understanding and modelling autumn phenology and carbon cycling under warming scenarios.
Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets
Authors: Lehtinen Markus J , Ritesh Kumar , Bryan Zabel , Mäkelä Sanna M , Derek Nedveck , Peipei Tang , Sinikka Latvala , Sebastien Guery , Budinoff Charles R 
Published: July 2021

SummaryProbiotics have been suggested as one solution to counter detrimental health effects by SARS-CoV-2, however, data so far is scarce. We tested the effect of two probiotic consortia, OL-1 and OL-2, against SARS-CoV-2 in ferrets and assessed their effect on cytokine production and transcriptome in a human monocyte-derived macrophage (Mf) and dendritic cell (DC) model.The results showed that the consortia significantly reduced the viral load, modulated immune response, and regulated viral receptor expression in ferrets compared to placebo. In human Mf and DC model, OL-1 and OL-2 induced cytokine production and genes related to SARS-CoV-2 anti-viral immunity.The study results indicate that probiotic stimulation of the ferret immune system leads to improved anti-viral immunity against SARS-COV-2 and that critical genes and cytokines for anti-SARS-CoV-2 immunity are stimulated in human immune cellsin vitro. The effect of the consortia against SARS-CoV-2 warrants further investigations in human clinical trials.
Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars
Authors: Layos John King N. , Geromo Ronel N. , Espina Dinah M. , Nishibori Masahide 
Published: July 2021

AbstractThe Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of pig dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with some human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine native pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boars corresponding to their geographic origin. Results revealed a considerable genetic diversity (0.900±0.016), and a widespread Asian pig-ancestry (94.60%) were revealed in the phylogenetic analysis with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine pigs corroborates our hypothesis of a genetic signal that could potentially be associated with the recently reported multiple waves of human migrations to the Philippines during the last 50,000 years. The high frequency of haplotypes (54.08%) that collapsed in the D7 haplogroup represent an interesting challenge as its distribution does not coincide with the hypothesized migratory route of the Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes which postulate the legitimate dispersal of pigs associated with the multiple waves of human migrations involving the Philippines. The multimodal mismatch and neutrality test statistics both Fu’s Fs and Tajima’s D correlates the long stationary period of effective population size revealed in the Bayesian skyline plot. While the sudden decrease in population was consistent with the pronounced population bottleneck of Asian and European pigs during the interglacial periods of the Pleistocene.
Molecular characterization and functional annotation of a hypothetical protein (TDB29877.1) from probiotic bacteria Lactobacillus acidophilus: an in-silico approach
Authors: Rabbani Md Ataul Goni 
Published: July 2021

AbstractLactobacillus acidophilus bacteria are widely used as probiotic and to produce various healthy fermented food products. The PNW3 strain of the bacteria has numerous proteins in its genome and some are considered as hypothetical proteins. The aim of the present study was to predict the structures and biological functions of the hypothetical protein (accession number: TDB29877.1) from L. acidophilus through an in-silico approach applying various bioinformatics tools. The sequence similarity was searched on the available biological databases using BLASTp program to find out the homologues proteins. Besides, determination of various properties like physicochemical characteristics, subcellular localization, phylogenetic analysis, functional annotation, protein-protein interaction, determination of secondary and tertiary structures, active site detection and further quality assessment analysis were done using appropriate computational methods of bioinformatics. In-silico analysis revealed that the hypothetical protein has contained TerB-N and TerB-C domains with the presence of YjbR-like superfamily. The Protein-protein interaction network analysis revealed that the protein highly interacted with various known and unknown proteins responsible for iron ion binding, DNA and RNA metabolisms and numerous repair mechanisms that maintain cellular integrity. It was also found that the protein has predominantly alpha-helices in its secondary structure and the three dimensional model has been found to be novel as it possessed expected quality while gone through various quality assessment tools. Thus, the present result indicated that the selected hypothetical protein which is cytoplasmic in nature with Belta-grasp fold, plays important role in responding during stress condition or phage defense mechanism.
miR-206 inhibits estrogen-induced proliferation and invasion of ER-α36 positive gastric cancer cells
Authors: Yuan Chunyan , Yang Yuanyuan , Jiang Xuebing , Xie Xiaoli , Liu Jun , Wang Xuming , Sheng Xia 
Published: July 2021

AbstractObjectiveTo explore the biological role of miR-206 in inhibiting the proliferation and invasion of estrogen-induced ER-α36 positive gastric cancer cells and its related mechanisms.MethodsMTT and tranwell assays were used to detect the proliferation and invasion of BGC-823 cells under different concentrations and time of ER stimulation. RT-PCR was used to detect the effect of ER stimulation on the content of miR-206 in gastric cancer cells. miR-206 mimics were transfected into BGC-823 cells to detect cell proliferation and invasion; luciferase reporter assay was used to determine whether miR-206 targets the 3’-untranslated region of the CDK14-encoding gene (3’ -UTR).ResultsWe confirmed that estrogen promoted the proliferation and invasion of BGC-823 cells; As the concentration of estrogen increases, the level of miR206 in the cell gradually rises.Overexpression of miR-206 significantly decreased the estrogen-induced BGC-823 cells. Proliferative and invasive ability; miR-206 inhibits the expression of CDK14 by directly binding to the 3’-UTR of CDK14 mRNA, thereby inhibiting the proliferation and invasion of gastric cancer cells.ConclusionsOur results suggest that miR-206 inhibits estrogen-induced proliferation and invasion of ER-α36-positive gastric cancer cells by inhibiting CDK14 and may be a promising therapeutic option for anticancer therapy.
Decoding the Neural Signatures of Valence and Arousal From Portable EEG Headset
Authors: Garg Nikhil , Garg Rohit , Anand Apoorv , Baths Veeky 
Published: July 2021

ABSTRACTEmotion classification using electroencephalography (EEG) data and machine learning techniques has been on the rise in the recent past. However, past studies uses data from medical-grade EEG setup with long set-up time and environment constraints. This paper focuses on classifying emotions on the valence-arousal plane using various feature extraction, feature selection and machine learning techniques. We evaluate different feature extraction and selection techniques and propose the optimal set of features and electrodes for emotion recognition. The images from the OASIS image dataset were used to elicit valence and arousal emotions, and the EEG data was recorded using the Emotiv Epoc X mobile EEG headset. The analysis is carried out on publicly available datasets: DEAP and DREAMER for benchmarking. We propose a novel feature ranking technique and incremental learning approach to analyze performance dependence on the number of participants. Leave-one-subject-out cross-validation was carried out to identify subject bias in emotion elicitation patterns. The importance of different electrode locations was calculated, which could be used for designing a headset for emotion recognition. The collected dataset and pipeline are also published. Our study achieved a root mean square score (RMSE) of 0.905 on DREAMER, 1.902 on DEAP, and 2.728 on our dataset for valence label and a score of 0.749 on DREAMER, 1.769 on DEAP and 2.3 on our proposed dataset for arousal label respectively.
Gastric cancer derived exosomes induce peritoneal mesothelial cell EMT through TGF-β1/Smads pathway to promote peritoneal metastasis
Authors: Dong Jungang , Zhu Zhongbo , Cui Guoning , Zhang Zhixuan , Yue Juan , Zhang Yinghong , Yao Xuehan , Huo Minfeng , Wei Jingjing , Wang Qingmiao , Dai Lirong , Li Peiqing , Liu Xi-Ping 
Published: July 2021

AbstractEpithelial-mesenchymal transition (EMT) plays an important role in peritoneal metastasis of Gastric cancer (GC). Tumor exosomes can mediate tumor directed metastasis, and TGF-β1 is an important factor in inducing tumor Epithelial mesenchymal transition. However, it is not clear whether GC derived exosomes can induce peritoneal mesothelial cells through the TGF-β1/ Smads pathway and the effect of injured peritoneal mesothelial cells on the biological characteristics of GC cells. In this study, we demonstrated that GC-derived exosomes can activate the TGF-β1/Smads pathway in peritoneal mesothelial cells and induce the corresponding EMT process, and that the injured peritoneal mesothelial cells can improve the migration and adhesion of GC cells. Taken together, these data further support the critical role of exosomes in the remodeling of the pre-metastatic microenvironment.
Synthesis and characterization of peptide conjugated human serum albumin nanoparticles for targeted cardiac uptake and drug delivery
Authors: Lomis Nikita , Westfall Susan , Shum-Tim Dominique , Prakash Satya 
Published: July 2021

AbstractCongestive heart failure, a prominent cardiovascular disease results primarily from myocardial infarction or ischemia. Milrinone (MRN), a widely used clinical drug for heart failure, improves myocardial contractility and cardiac function through its inotropic and vasodilatory effects. However, lacking target specificty, it exhibits low bioavailability and lower body retention time. Therefore, in this study, angiotensin II (AT1) peptide conjugated human serum albumin nanoparticles (AT1-HSA-MRN-NPs) have been synthesized for targeted delivery of MRN to the myocardium, overexpressing AT1 receptors under heart failure. The NPs were surface functionalized through a covalent conjugation reaction between HSA and AT1. Nanoparticle size was 215.2±4.7 nm and zeta potential -28.8±2.7 mV and cumulative release of MRN was ∼72% over 24 hrs. The intracellular uptake of nanoparticles and cell viability was studied in H9c2 cells treated with AT1-MRN-HSA-NPs vs the control non-targeted drug, MRN Lactate under normal, hypoxic and hypertrophic conditions. The uptake of AT1-HSA-MRN-NPs in H9c2 cells was significantly higher as compared to non-targeted nanoparticles, and the viability of H9c2 cells treated with AT1-MRN-HSA-NPs vs MRN Lactate was 73.4±1.4% vs 44.9±1.4%, respectively. Therefore, AT1-HSA-MRN-NPs are safe for in vivo use and exhibit superior targeting and drug delivery characteristics for treatment of heart failure.