bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primate-specific transposable elements shape transcriptional networks during human development
Authors: Pontis Julien , Pulver Cyril , Playfoot Christopher J. , Planet Evarist , Grun Delphine , Offner Sandra , Duc Julien , Manfrin Andrea , Lutolf Matthias P. , Trono Didier 
Published: November 2022

AbstractThe human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
Biomimetic electrodynamic nanoparticles comprising ginger-derived extracellular vesicles for synergistic anti-infective therapy
Authors: Qiao Zhuangzhuang , Zhang Kai , Liu Jin , Cheng Daojian , Yu Bingran , Zhao Nana , Xu Fu-Jian 
Published: November 2022

AbstractNanotechnology enlightens promising antibacterial strategies while the complex in vivo infection environment poses a great challenge to the rational design of nanoplatforms for safe and effective anti-infective therapy. Herein, a biomimetic nanoplatform (EV-Pd-Pt) integrating electrodynamic Pd-Pt nanosheets and natural ginger-derived extracellular vesicles (EVs) is proposed. The introduction of ginger-derived EVs greatly endows EV-Pd-Pt with prolonged blood circulation without immune clearance, as well as accumulation at infection sites. More interestingly, EV-Pd-Pt can enter the interior of bacteria in an EV lipid-dependent manner. At the same time, reactive oxygen species are sustainably generated in situ to overcome the limitations of their short lifetime and diffusion distance. Notably, EV-Pd-Pt nanoparticle-mediated electrodynamic and photothermal therapy exhibit synergistic effects. Furthermore, the desirable biocompatibility and biosafety of the proposed nanoplatform guarantee the feasibility of in vivo applications. This proof-of-concept work holds significant promise for developing biomimetic nanoparticles by exploiting their intrinsic properties for synergistic anti-infective therapy.
Chromosome segregation fidelity requires microtubule polyglutamylation by the cancer downregulated enzyme TTLL11
Authors: Zadra Ivan , Jimenez-Delgado Senda , Anglada-Girotto Miquel , Segura-Morales Carolina , Compton Zachary J. , Janke Carsten , Serrano Luis , Ruprecht Verena , Vernos Isabelle 
Published: November 2022

AbstractRegulation of microtubule (MT) dynamics is key for mitotic spindle assembly and faithful chromosome segregation. Here we show that polyglutamylation, a still understudied post-translational modification of spindle MTs, is essential to define their dynamics within the range required for error-free chromosome segregation. We identify TTLL11 as an enzyme driving MT polyglutamylation in mitosis and show that reducing TTLL11 levels in human cells or zebrafish embryos compromises chromosome segregation fidelity and impairs early embryonic development. Our data reveal a mechanism to ensure genome stability in normal cells that is compromised in cancer cells that systematically downregulate TTLL11. Our data suggest a direct link between MT dynamics regulation, MT polyglutamylation and two salient features of tumour cells, aneuploidy and chromosome instability (CIN).
A non-coding GWAS variant impacts anthracycline-induced cardiotoxic phenotypes in human iPSC-derived cardiomyocytes
Authors: Wu Xi , Shen Fei , Jiang Guanglong , Xue Gloria , Philips Santosh , Gardner Laura , Cunningham Geneva , Bales Casey , Cantor Erica , Schneider Bryan Paul 
Published: November 2022

AbstractAnthracyclines, widely used to treat breast cancer, have the potential for cardiotoxicity. We have previously identified and validated a germline single nucleotide polymorphism, rs28714259, associated with an increased risk of anthracycline-induced heart failure. We now provide insights into the mechanism by which rs28714259 might confer increased risk of cardiac damage. Using hiPSC-derived cardiomyocyte cell lines with either intrinsic polymorphism or CRISPR-Cas9-mediated deletion of rs28714259 locus, we demonstrate that glucocorticoid receptor signaling activated by dexamethasone pretreatment prior to doxorubicin exposure preserves cardiomyocyte viability and contractility in cardiomyocytes containing the major allele. Homozygous loss of the rs28714259 major allele diminishes dexamethasone’s protective effect. We further demonstrate that the risk allele of rs28714259 disrupts glucocorticoid receptor and rs28714259 binding affinity. Finally, we highlight the activation of genes and pathways involved in cardiac hypertrophy signaling that are blocked by the risk allele, suggesting a decreased adaptive survival response to doxorubicin-related stress.
Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis
Authors: Ruiz Mario , Devkota Ranjan , Panagaki Dimitra , Bergh Per-Olof , Kaper Delaney , Henricsson Marcus , Nik Ali , Petkevicius Kasparas , Höög Johanna L. , Bohlooly-Y Mohammad , Carlsson Peter , Borén Jan , Pilon Marc 
Published: November 2022

AbstractCells and organisms require proper membrane composition to function and develop. Phospholipids are the major component of membranes and are primarily acquired through the diet. Given great variability in diet composition, cells must be able to deploy mechanisms that correct deviations from optimal membrane composition and properties. Here, using lipidomics and unbiased proteomics, we found that the embryonic lethality in mice lacking the fluidity regulators Adiponectin Receptors 1 and 2 (AdipoR1/2) is associated with aberrant high saturation of the membrane phospholipids. Using mouse embryonic fibroblasts (MEFs) derived from AdipoR1/2-KO embryos, human cell lines and the model organism C. elegans we found that, mechanistically, AdipoR1/2-derived sphingosine 1-phosphate (S1P) signals in parallel through S1PR3-SREBP1 and PPARγ to sustain the expression of the fatty acid desaturase SCD and maintain membrane properties. Thus, our work identifies an evolutionary conserved pathway by which cells and organisms achieve membrane homeostasis and adapt to a variable environment.
Wildflower phenological escape differs by continent and spring temperature
Authors: Lee Benjamin R. , Miller Tara K. , Rosche Christoph , Yang Yong , Heberling J. Mason , Kuebbing Sara E. , Primack Richard B. 
Published: November 2022

AbstractTemperate understory plant species are at risk from climate change and anthropogenic threats that include increased deer herbivory, habitat loss, pollinator declines and mismatch, and nutrient pollution. Recent work suggests that spring ephemeral wildflowers may be at additional risk due to phenological mismatch with deciduous canopy trees. The study of this dynamic, commonly referred to as “phenological escape”, and its sensitivity to spring temperature is limited to eastern North America. Here, we use herbarium specimens to show that phenological sensitivity to spring temperature is remarkably conserved for understory wildflowers across North America, Europe, and Asia, but that canopy trees in North America are significantly more sensitive to spring temperature compared to in Asia and Europe. We predict that advancing tree phenology will lead to decreasing spring light windows in North America while spring light windows will be maintained or even increase in Asia and Europe in response to projected climate warming.
Unraveling sulfur chemistry in interstellar carbon oxide ices
Authors: Li Xiaolong , Lu Bo , Wang Lina , Xue Junfei , Zhu Bifeng , Trabelsi Tarek , Francisco Joseph S. , Zeng Xiaoqing 
Published: November 2022

AbstractFormyl radical (HCO•) and hydroxycarbonyl radical (HOCO•) are versatile building blocks in the formation of biorelevant complex organic molecules (COMs) in interstellar medium. Understanding the chemical pathways for the formation of HCO• and HOCO• starting with primordial substances (e.g., CO and CO2) is of vital importance in building the complex network of prebiotic chemistry. Here, we report the efficient formation of HCO• and HOCO• in the photochemistry of hydroxidooxidosulfur radical (HOSO•)–a key intermediate in SO2photochemistry–in interstellar analogous ices of CO and CO2at 16 K through hydrogen atom transfer (HAT) reactions. Specifically, 266 nm laser photolysis of HOSO• embedded in solid CO ice yields the elusive hydrogen‑bonded complexes HCO•···SO2and HOCO•···SO, and the latter undergoes subsequent HAT to furnish CO2···HOS• under the irradiation conditions. Similar photo-induced HAT of HOSO• in solid CO2ice leads to the formation of HOCO•···SO2. The HAT reactions of HOSO• in astronomical CO and CO2ices by forming reactive acyl radicals may contribute to understanding the interplay between the sulfur and carbon ice-grain chemistry in cold molecular clouds and also in the planetary atmospheric chemistry.
Spatially nanoconfined N-type polymer semiconductors for stretchable ultrasensitive X-ray detection
Authors: Bian Yangshuang , Liu Kai , Ran Yang , Li Yi , Gao Yuanhong , Zhao Zhiyuan , Shao Mingchao , Liu Yanwei , Kuang Junhua , Zhu Zhiheng , Qin Mingcong , Pan Zhichao , Zhu Mingliang , Wang Chenyu , Chen Hu , Li Jia , Li Xifeng , Liu Yunqi , Guo Yunlong 
Published: November 2022

AbstractPolymer semiconductors are promising candidates for wearable and skin-like X-ray detectors due to their scalable manufacturing, adjustable molecular structures and intrinsic flexibility. Herein, we fabricated an intrinsically stretchable n-type polymer semiconductor through spatial nanoconfinement effect for ultrasensitive X-ray detectors. The design of high-orientation nanofiber structures and dense interpenetrating polymer networks enhanced the electron-transporting efficiency and stability of the polymer semiconductors. The resultant polymer semiconductors exhibited an ultrahigh sensitivity of 1.52 × 104 μC Gyair−1 cm−2, an ultralow detection limit of 37.7 nGyair s−1 (comparable to the record-low value of perovskite single crystals), and polymer film X-ray imaging was achieved at a low dose rate of 3.65 μGyair s−1 (about 1/12 dose rate of the commercial medical chest X-ray diagnosis). Meanwhile, the hybrid semiconductor films could sustain 100% biaxial stretching strain with minimal degeneracy in photoelectrical performances. These results provide insights into future high-performance, low-cost e-skin photoelectronic detectors and imaging.
A distinct ripple-formation regime on Mars revealed by the morphometrics of barchan dunes
Authors: Rubanenko Lior , Lapôtre Mathieu G. A. , Ewing Ryan C. , Fenton Lori K. , Gunn Andrew 
Published: November 2022

AbstractSand mobilized by wind forms decimeter-scale impact ripples and decameter-scale or larger dunes on Earth and Mars. In addition to those two bedform scales, orbital and in situ images revealed a third distinct class of larger meter-scale ripples on Mars. Since their discovery, two main hypotheses have been proposed to explain the formation of large martian ripples—that they originate from the growth in wavelength and height of decimeter-scale ripples or that they arise from the same hydrodynamic instability as windblown dunes or subaqueous bedforms instead. Here we provide evidence that large martian ripples form from the same hydrodynamic instability as windblown dunes and subaqueous ripples. Using an artificial neural network, we characterize the morphometrics of over a million isolated barchan dunes on Mars and analyze how their size and shape vary across Mars’ surface. We find that the size of Mars’ smallest dunes decreases with increasing atmospheric density with a power-law exponent predicted by hydrodynamic theory, similarly to meter-size ripples, tightly bounding a forbidden range in bedform sizes. Our results provide key evidence for a unifying model for the formation of subaqueous and windblown bedforms on planetary surfaces, offering a new quantitative tool to decipher Mars’ atmospheric evolution.
The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB
Authors: Steiner Elisabeth , Shilling Rebecca E. , Richter Anja M. , Schmid Nadine , Fazli Mustafa , Kaever Volkhard , Jenal Urs , Tolker-Nielsen Tim , Eberl Leo 
Published: November 2022

AbstractThe polysaccharide Bep is essential for in vitro biofilm formation of the opportunistic pathogen Burkholderia cenocepacia. We found that the Burkholderia diffusible signaling factor (BDSF) quorum sensing receptor RpfR is a negative regulator of the bep gene cluster in B. cenocepacia. An rpfR mutant formed wrinkled colonies, whereas additional mutations in the bep genes or known bep regulators like berA and berB restored the wild-type smooth colony morphology. We found that there is a good correlation between intracellular c-di-GMP levels and bep expression when the c-di-GMP level is increased or decreased through ectopic expression of a diguanylate cyclase or a c-di-GMP phosphodiesterase, respectively. However, when the intracellular c-di-GMP level is changed by site directed mutagenesis of the EAL or GGDEF domain of RpfR there is no correlation between intracellular c-di-GMP levels and bep expression. Except for rpfR, deletion mutants of all 25 c-di-GMP phosphodiesterase and diguanylate cyclase genes encoded by B. cenocepacia showed no change to berA and bep gene expression. Moreover, bacterial two-hybrid assays provided evidence that RpfR and BerB physically interact and give specificity to the regulation of the bep genes. We suggest a model where RpfR binds BerB at low c-di-GMP levels to sequester this RpoN-dependent activator to an RpfR/RpfF complex. If the c-di-GMP levels rise, possibly by the enzymatic action of RpfR, BerB binds c-di-GMP and is released from the RpfR/RpfF complex and associates with RpoN to activate transcription of berA, and the BerA protein subsequently activates transcription of the bep genes.
Oxidative stability and sensory evaluation of sodium caseinate-based yak butter powder
Authors: Agyare Anita N. , Liang Qi , Song Xuemei , Zhang Yan , Yang Jing , Shi Yongqi 
Published: November 2022

AbstractYak butter’s high unsaturated fatty acid level predisposes it to oxidation, hence must be converted into more stable forms like powder. This study aimed to spray dry yak butter using 10% yak butter and four sodium caseinate (NaCas) formulations: sample A: 100% NaCas; sample B: 50% NaCas, 50% lactose; sample C: 75% NaCas, 25% lactose; and sample D: 25% NaCas, 75% maltodextrin. The powders were vacuum and hermetically sealed, and evaluated for oxidative stability, physical and sensory properties during storage at 65 ℃ for 30 days. The results showed that samples B and D had similar and most favorable physical properties (such as, moisture, water activity, particle size, bulk density re-dispersion time, and encapsulation efficiency); though sample B, together with sample C, browned the most during storage. The majority of the sensory panelists preferred samples B and D; observed high caking in samples C and B; and the least whiteness loss and caking in samples D and A but high off-flavors in samples A and C. After storage, peroxide and thiobarbituric acid values of powder samples ranged from 34.98 to 69.54 meqO2/kg and 1.85–9.43 mg MD/kg, respectively, in the decreasing order of A, C, B, and D. Sample D, followed by B, showed the highest radical scavenging activity. Therefore, for optimum yak butter powder physical properties and oxidative stability, 50%:50%, NaCas: lactose, and 25%:75%, NaCas: maltodextrin formulations should be used. This study provides essential knowledge for butter powder processors.
Extinction magnitude of animals in the near future
Authors: Kaiho Kunio 
Published: November 2022

AbstractThere have been five major mass extinctions and some minor mass extinctions of animals since early animal diversification 540–520 Myr ago. It is said that a sixth mass extinction is already underway. However, the future extinction magnitude has not been quantitatively estimated. Here, I show that the sixth major mass extinction (defined as > 60% species loss) will be avoided, but a minor mass extinction, 20–50% animal species loss (1% now), will occur when humans cause nuclear war and/or fail to stop increasing greenhouse gas (GHG) emissions, pollution, and deforestation until 2060–2080 CE. When humans decrease GHG emissions, pollution, and deforestation in 40 years and prevent nuclear war in the future, 10–15% animal species loss will occur. Humans should stop not only industrial GHG emissions but also deforestation, environmental pollution, and nuclear war to prevent this mass extinction. When humans fail to stop these processes, significant decreases in biodiversity and the human population and a collapse of ecological balance will occur on Earth.
Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients
Authors: Ivanisenko V. A. , Gaisler E. V. , Basov N. V. , Rogachev A. D. , Cheresiz S. V. , Ivanisenko T. V. , Demenkov P. S. , Mishchenko E. L. , Khripko O. P. , Khripko Yu. I. , Voevoda S. M. , Karpenko T. N. , Velichko A. J. , Voevoda M. I. , Kolchanov N. A. , Pokrovsky A. G. 
Published: November 2022

AbstractMetabolomic analysis of blood plasma samples from COVID-19 patients is a promising approach allowing for the evaluation of disease progression. We performed the metabolomic analysis of plasma samples of 30 COVID-19 patients and the 19 controls using the high-performance liquid chromatography (HPLC) coupled with tandem mass spectrometric detection (LC–MS/MS). In our analysis, we identified 103 metabolites enriched in KEGG metabolic pathways such as amino acid metabolism and the biosynthesis of aminoacyl-tRNAs, which differed significantly between the COVID-19 patients and the controls. Using ANDSystem software, we performed the reconstruction of gene networks describing the potential genetic regulation of metabolic pathways perturbed in COVID-19 patients by SARS-CoV-2 proteins. The nonstructural proteins of SARS-CoV-2 (orf8 and nsp5) and structural protein E were involved in the greater number of regulatory pathways. The reconstructed gene networks suggest the hypotheses on the molecular mechanisms of virus-host interactions in COVID-19 pathology and provide a basis for the further experimental and computer studies of the regulation of metabolic pathways by SARS-CoV-2 proteins. Our metabolomic analysis suggests the need for nonstructural protein-based vaccines and the control strategy to reduce the disease progression of COVID-19.
Identification of potentially functional modules and diagnostic genes related to amyotrophic lateral sclerosis based on the WGCNA and LASSO algorithms
Authors: Daneshafrooz Narges , Bagherzadeh Cham Masumeh , Majidi Mohammad , Panahi Bahman 
Published: November 2022

AbstractAmyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases’, ‘amyotrophic lateral sclerosis’, and ‘endocytosis’ KEGG terms. Further, some of other modules related to ALS were enriched in ‘autophagy’ and ‘amyotrophic lateral sclerosis’. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.
Size-dependent bioactivity of electrosprayed core–shell chitosan-alginate particles for protein delivery
Authors: Shamszadeh Sayna , Akrami Mohammad , Asgary Saeed 
Published: November 2022

AbstractNano-bio interactions are size-dependent. The present study investigates whether core–shell chitosan-alginate particle size governs biological activities as well as protein release profile. A coaxial electrospraying was used to fabricate bovine serum albumin (BSA)-loaded core–shell micro/nanoparticles and were fully characterized. The bio/hemocompatibility of the particles was assessed using MTT and hemolytic assays, respectively, followed by the uptake assessment using flow cytometry. Finally, protein absorption was investigated using SDS-PAGE. The SEM size of the microparticles, the hydrodynamic, and the actual sizes of the nanoparticles were 1.2 μm, 90.49 nm, and 50 nm, respectively. Interactions among two polymers and BSA were observed using DSC analysis. BET analysis showed a more surface area for nanoparticles. A sustained release trend of BSA was observed after 14- and 10-day for microparticles and nanoparticles, respectively. Microparticles exhibited excellent hemocompatibility (< 5% hemolysis) and cell viability (at least > 70%) in all concentrations. However, acceptable hemolytic activity and cell viability were observed for nanoparticles in concentrations below 250 μg/mL. Furthermore, nanoparticles showed greater cellular uptake (~ 4 folds) and protein absorption (~ 1.61 folds) than microparticles. Overall, the developed core–shell chitosan-alginate particles in the micro/nanoscale can be promising candidates for biomedical application and regenerative medicine regarding their effects on above mentioned biological activities.