bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of plant phototropic growth by NPH3/RPT2-like substrate phosphorylation and 14-3-3 binding
Authors: Sullivan Stuart , Waksman Thomas , Paliogianni Dimitra , Henderson Louise , Lütkemeyer Melanie , Suetsugu Noriyuki , Christie John M. 
Published: October 2021

AbstractPolarity underlies all directional growth responses in plants including growth towards the light (phototropism). The plasma-membrane associated protein, NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) is a key determinant of phototropic growth which is regulated by phototropin (phot) AGC kinases. Here we demonstrate that NPH3 is directly phosphorylated by phot1 within a conserved C-terminal consensus sequence (RxS) that is necessary to promote phototropism and petiole positioning in Arabidopsis. RxS phosphorylation also triggers 14-3-3 binding combined with changes in NPH3 phosphorylation and localisation status. Mutants of NPH3 that are unable to bind or constitutively bind 14-3-3 s show compromised functionality consistent with a model where phototropic curvature is established by signalling outputs arising from a gradient of NPH3 RxS phosphorylation across the stem. Our findings therefore establish that NPH3/RPT2-Like (NRL) proteins are phosphorylation targets for plant AGC kinases. Moreover, RxS phosphorylation is conserved in other members of the NRL family, suggesting a common mechanism of regulating plant growth to the prevailing light environment.
Asthma-associated genetic variants induce IL33 differential expression through an enhancer-blocking regulatory region
Authors: Aneas Ivy , Decker Donna C. , Howard Chanie L. , Sobreira Débora R. , Sakabe Noboru J. , Blaine Kelly M. , Stein Michelle M. , Hrusch Cara L. , Montefiori Lindsey E. , Tena Juan , Magnaye Kevin M. , Clay Selene M. , Gern James E. , Jackson Daniel J. , Altman Matthew C. , Naureckas Edward T. , Hogarth Douglas K. , White Steven R. , Gomez-Skarmeta Jose Luis , Schoetler Nathan , Ober Carole , Sperling Anne I. , Nóbrega Marcelo A. 
Published: October 2021

AbstractGenome-wide association studies (GWAS) have implicated the IL33 locus in asthma, but the underlying mechanisms remain unclear. Here, we identify a 5 kb region within the GWAS-defined segment that acts as an enhancer-blocking element in vivo and in vitro. Chromatin conformation capture showed that this 5 kb region loops to the IL33 promoter, potentially regulating its expression. We show that the asthma-associated single nucleotide polymorphism (SNP) rs1888909, located within the 5 kb region, is associated with IL33 gene expression in human airway epithelial cells and IL-33 protein expression in human plasma, potentially through differential binding of OCT-1 (POU2F1) to the asthma-risk allele. Our data demonstrate that asthma-associated variants at the IL33 locus mediate allele-specific regulatory activity and IL33 expression, providing a mechanism through which a regulatory SNP contributes to genetic risk of asthma.
Integrated cooling (i-Cool) textile of heat conduction and sweat transportation for personal perspiration management
Authors: Peng Yucan , Li Wei , Liu Bofei , Jin Weiliang , Schaadt Joseph , Tang Jing , Zhou Guangmin , Wang Guanyang , Zhou Jiawei , Zhang Chi , Zhu Yangying , Huang Wenxiao , Wu Tong , Goodson Kenneth E. , Dames Chris , Prasher Ravi , Fan Shanhui , Cui Yi 
Published: October 2021

AbstractPerspiration evaporation plays an indispensable role in human body heat dissipation. However, conventional textiles tend to focus on sweat removal and pay little attention to the basic thermoregulation function of sweat, showing limited evaporation ability and cooling efficiency in moderate/profuse perspiration scenarios. Here, we propose an integrated cooling (i-Cool) textile with unique functional structure design for personal perspiration management. By integrating heat conductive pathways and water transport channels decently, i-Cool exhibits enhanced evaporation ability and high sweat evaporative cooling efficiency, not merely liquid sweat wicking function. In the steady-state evaporation test, compared to cotton, up to over 100% reduction in water mass gain ratio, and 3 times higher skin power density increment for every unit of sweat evaporation are demonstrated. Besides, i-Cool shows about 3 °C cooling effect with greatly reduced sweat consumption than cotton in the artificial sweating skin test. The practical application feasibility of i-Cool design principles is well validated based on commercial fabrics. Owing to its exceptional personal perspiration management performance, we expect the i-Cool concept can provide promising design guidelines for next-generation perspiration management textiles.
Orexin-A and endocannabinoids are involved in obesity-associated alteration of hippocampal neurogenesis, plasticity, and episodic memory in mice
Authors: Forte Nicola , Boccella Serena , Tunisi Lea , Fernández-Rilo Alba Clara , Imperatore Roberta , Iannotti Fabio Arturo , De Risi Maria , Iannotta Monica , Piscitelli Fabiana , Capasso Raffaele , De Girolamo Paolo , De Leonibus Elvira , Maione Sabatino , Di Marzo Vincenzo , Cristino Luigia 
Published: October 2021

AbstractThe mammalian brain stores and distinguishes among episodic memories, i.e. memories formed during the personal experience, through a mechanism of pattern separation computed in the hippocampal dentate gyrus. Decision-making for food-related behaviors, such as the choice and intake of food, might be affected in obese subjects by alterations in the retrieval of episodic memories. Adult neurogenesis in the dentate gyrus regulates the pattern separation. Several molecular factors affect adult neurogenesis and exert a critical role in the development and plasticity of newborn neurons. Orexin-A/hypocretin-1 and downstream endocannabinoid 2-arachidonoylglycerol signaling are altered in obese mice. Here, we show that excessive orexin-A/2-arachidonoylglycerol/cannabinoid receptor type-1 signaling leads to the dysfunction of adult hippocampal neurogenesis and the subsequent inhibition of plasticity and impairment of pattern separation. By inhibiting orexin-A action at orexin-1 receptors we rescued both plasticity and pattern separation impairment in obese mice, thus providing a molecular and functional mechanism to explain alterations in episodic memory in obesity.
IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies
Authors: Friedrich Matthias , Pohin Mathilde , Jackson Matthew A. , Korsunsky Ilya , Bullers Samuel J. , Rue-Albrecht Kevin , Christoforidou Zoe , Sathananthan Dharshan , Thomas Tom , Ravindran Rahul , Tandon Ruchi , Peres Raphael Sanches , Sharpe Hannah , Wei Kevin , Watts Gerald F. M. , Mann Elizabeth H. , Geremia Alessandra , Attar Moustafa ,   Oxford IBD Cohort Investigators,   Roche Fibroblast Network Consortium, Barone Francesca , Brenner Michael , Buckley Christopher D. , Coles Mark , Frei Andreas P. , Lassen Kara G. , Powrie Fiona M. , McCuaig Sarah , Thomas Lloyd , Collantes Elena , Uhlig Holm H. , Sansom Stephen N. , Easton Alistair , Raychaudhuri Soumya , Travis Simon P. , Powrie Fiona M. 
Published: October 2021

AbstractCurrent inflammatory bowel disease (IBD) therapies are ineffective in a high proportion of patients. Combining bulk and single-cell transcriptomics, quantitative histopathology and in situ localization across three cohorts of patients with IBD (total n = 376), we identify coexpressed gene modules within the heterogeneous tissular inflammatory response in IBD that map to distinct histopathological and cellular features (pathotypes). One of these pathotypes is defined by high neutrophil infiltration, activation of fibroblasts and vascular remodeling at sites of deep ulceration. Activated fibroblasts in the ulcer bed display neutrophil-chemoattractant properties that are IL-1R, but not TNF, dependent. Pathotype-associated neutrophil and fibroblast signatures are increased in nonresponders to several therapies across four independent cohorts (total n = 343). The identification of distinct, localized, tissular pathotypes will aid precision targeting of current therapeutics and provides a biological rationale for IL-1 signaling blockade in ulcerating disease.
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns
Authors: Feldmesser Ester , Ben-Dor Shifra , Vardi Assaf 
Published: October 2021

AbstractEmiliania huxleyi is a cosmopolitan coccolithophore widespread in temperate oceans. This unicellular photoautotroph forms massive recurring blooms that play an important role in large biogeochemical cycles of carbon and sulfur, which play a role in climate change. The mechanism of bloom formation and demise, controlled by giant viruses that routinely infect these blooms, is poorly understood. We generated a pan-transcriptome of E. huxleyi, derived from three strains with different susceptibility to viral infection. Expression profiling of E. huxleyi sensitive and resistant strains showed major basal differences, including many genes that are induced upon viral infection. This suggests that basal gene expression can affect the host metabolic state and the susceptibility of E. huxleyi to viruses. Due to its ecological importance, the pan-transcriptome and its protein translation, applicable to many E. huxleyi strains, is a powerful resource for investigation of eukaryotic microbial communities.
Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens
Authors: Ju Xiaojun , Liu Yifan , Shan Yanju , Ji Gaige , Zhang Ming , Tu Yunjie , Zou Jianmin , Chen Xingyong , Geng Zhaoyu , Shu Jingting 
Published: October 2021

AbstractSART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.
Interindividual heterogeneity affects the outcome of human cardiac tissue decellularization
Authors: Tenreiro Miguel F. , Almeida Henrique V. , Calmeiro Tomás , Fortunato Elvira , Ferreira Lino , Alves Paula M. , Serra Margarida 
Published: October 2021

AbstractThe extracellular matrix (ECM) of engineered human cardiac tissues corresponds to simplistic biomaterials that allow tissue assembly, or animal derived off-the-shelf non-cardiac specific matrices. Decellularized ECM from human cardiac tissue could provide a means to improve the mimicry of engineered human cardiac tissues. Decellularization of cardiac tissue samples using immersion-based methods can produce acceptable cardiac ECM scaffolds; however, these protocols are mostly described for animal tissue preparations. We have tested four methods to decellularize human cardiac tissue and evaluated their efficiency in terms of cell removal and preservation of key ECM components, such as collagens and sulfated glycosaminoglycans. Extended exposure to decellularization agents, namely sodium dodecyl sulfate and Triton-X-100, was needed to significantly remove DNA content by approximately 93% in all human donors. However, the biochemical composition of decellularized tissue is affected, and the preservation of ECM architecture is donor dependent. Our results indicate that standardization of decellularization protocols for human tissue is likely unfeasible, and a compromise between cell removal and ECM preservation must be established in accordance with the scaffold’s intended application. Notwithstanding, decellularized human cardiac ECM supported human induced pluripotent-derived cardiomyocyte (hiPSC-CM) attachment and retention for up to 2 weeks of culture, and promoted cell alignment and contraction, providing evidence it could be a valuable tool for cardiac tissue engineering.
Dual recombinase action in the normal and neoplastic mammary gland epithelium
Authors: Rädler Patrick D. , Vistisen Kerry , Triplett Aleata A. , Dennaoui Rayane , Li Yong , Shrestha Hridaya , Ferraiuolo Rosa-Maria , Thangasamy Amalraj , Saur Dieter , Wagner Kay-Uwe 
Published: October 2021

AbstractWe developed a transgenic mouse line that expresses the codon-optimized Flp recombinase under the control of the MMTV promoter in luminal epithelial cells of the mammary gland. In this report, we demonstrate the versatile applicability of the new MMTV-Flp strain to manipulate genes in a temporally and spatially controlled manner in the normal mammary gland, in luminal-type mammary tumors that overexpress ERBB2, and in a new KRAS-associated mammary cancer model. Although the MMTV-Flp is expressed in a mosaic pattern in the luminal epithelium, the Flp-mediated activation of a mutant KrasG12D allele resulted in basal-like mammary tumors that progressively acquired mesenchymal features. Besides its applicability as a tool for gene activation and cell lineage tracing to validate the cellular origin of primary and metastatic tumor cells, we employed the MMTV-Flp transgene together with the tamoxifen-inducible Cre recombinase to demonstrate that the combinatorial action of both recombinases can be used to delete or to activate genes in established tumors. In a proof-of-principle experiment, we conditionally deleted the JAK1 tyrosine kinase in KRAS-transformed mammary cancer cells using the dual recombinase approach and found that lack of JAK1 was sufficient to block the constitutive activation of STAT3. The collective results from the various lines of investigation showed that it is, in principle, feasible to manipulate genes in a ligand-controlled manner in neoplastic mammary epithelial cells, even when cancer cells acquire a state of cellular plasticity that may no longer support the expression of the MMTV-Flp transgene.
Antimicrobial activity and mode of action of 1,8-cineol against carbapenemase-producing Klebsiella pneumoniae
Authors: Moo Chew-Li , Osman Mohd Azuraidi , Yang Shun-Kai , Yap Wai-Sum , Ismail Saila , Lim Swee-Hua-Erin , Chong Chou-Min , Lai Kok-Song 
Published: October 2021

AbstractAntimicrobial resistance remains one of the most challenging issues that threatens the health of people around the world. Plant-derived natural compounds have received considerable attention for their potential role to mitigate antibiotic resistance. This study was carried out to assess the antimicrobial activity and mode of action of a monoterpene, 1,8-cineol (CN) against carbapenemase-producing Klebsiella pneumoniae (KPC-KP). Results showed that resazurin microplate assay and time-kill analysis revealed bactericidal effects of CN at 28.83 mg/mL. Zeta potential showed that CN increased the surface charge of bacteria and an increase of outer membrane permeability was also detected. CN was able to cause leakage of proteins and nucleic acids in KPC-KP cells upon exposure to CN and ethidium bromide influx/efflux experiment showed the uptake of ethidium bromide into the cell; this was attributed to membrane damage. CN was also found to induce oxidative stress in CN-treated KPC-KP cells through generation of reactive oxygen species which initiated lipid peroxidation and thus damaging the bacterial cell membrane. Scanning and transmission electron microscopies further confirmed the disruption of bacterial cell membrane and loss of intracellular materials. In this study, we demonstrated that CN induced oxidative stress and membrane damage resulting in KPC-KP cell death.
Sake yeast induces the sleep-promoting effects under the stress-induced acute insomnia in mice
Authors: Nishimon Shohei , Sakai Noriaki , Nishino Seiji 
Published: October 2021

AbstractSleep deprivation induces adverse effects on the health, productivity, and performance. The individuals who could not get enough sleep temporarily experience the symptoms of an induced acute insomnia. This study investigated the efficacy of sake yeast in treatment of acute insomnia in mice. The results of this study showed that sake yeast induced a significant dose-dependent wake reduction, a rapid eye movement (REM) and a non-REM (NREM) sleep enhancement during the first 6 h after the oral administration of sake yeast with locomotor activity and core body temperature decreases under the stressful environment in a new cage. In fact, the wake amounts at 3 h and 6 h were significantly reduced after the oral administration of sake yeast compared with the vehicle. The NREM sleep amounts at 3 h and 6 h significantly increased after the administration of sake yeast compared with the vehicle. The REM amount at 6 h significantly increased after the administration of sake yeast compared with the vehicle, but not at 3 h. The previous study suggested that the sleep-promoting effects of sake yeast could be referred from the activating effect of adenosine A2A receptor (A2AR). In summary, the sake yeast is an A2AR agonist and may induce sleep due to its stress-reducing and anti-anxiety properties. Further verification of the involvement of adenosine in the pathophysiology of insomnia is needed.
Asymmetric optical cryptosystem for multiple images based on devil’s spiral Fresnel lens phase and random spiral transform in gyrator domain
Authors: Chen Hang , Liu Zhengjun , Tanougast Camel , Blondel Walter 
Published: October 2021

AbstractAn asymmetric cryptosystem is presented for encrypting multiple images in gyrator transform domains. In the encryption approach, the devil’s spiral Fresnel lens variable pure phase mask is first designed for each image band to be encrypted by using devil’ mask, random spiral phase and Fresnel mask, respectively. Subsequently, a novel random devil’ spiral Fresnel transform in optical gyrator transform is implemented to achieved the intermediate output. Then, the intermediate data is divided into two masks by employing random modulus decomposition in the asymmetric process. Finally, a random permutation matrix is utilized to obtain the ciphertext of the intact algorithm. For the decryption approach, two divided masks (private key and ciphertext) need to be imported into the optical gyrator input plane simultaneously. Some numerical experiments are given to verify the effectiveness and capability of this asymmetric cryptosystem.
Inferring a causal relationship between ceramide levels and COVID-19 respiratory distress
Authors: Khodadoust Mehran M. 
Published: October 2021

AbstractA causal relationship between plasma ceramide concentration and respiratory distress symptoms in COVID-19 patients is inferred. In this study, plasma samples of 52 individuals infected with COVID-19 were utilized in a lipidomic analysis. Lipids belonging to the ceramide class exhibited a 400-fold increase in total plasma concentration in infected patients. Further analysis led to the demonstration of concentration dependency for severe COVID-19 respiratory symptoms in a subclass of ceramides. The subclasses Cer(d18:0/24:1), Cer(d18:1/24:1), and Cer(d18:1/22:0) were shown to be increased by 48-, 40-, and 33-fold, respectively, in infected plasma samples and to 116-, 91- and 50-fold, respectively, in plasma samples with respiratory distress. Hence, monitoring plasma ceramide concentration, can be a valuable tool for measuring effects of therapies on COVID-19 respiratory distress patients.
Potential efficacy of existing drug molecules against severe fever with thrombocytopenia syndrome virus: an in silico study
Authors: Chatterjee Shilpa , Kim Choon-Mee , Kim Dong-Min 
Published: October 2021

AbstractSevere fever with thrombocytopenia syndrome (SFTS) is a zoonotic disease caused by the SFTS virus (SFTSV). SFTS can be considered a life-threatening notifiable infectious disease. The unavailability of specific therapeutics encourages the investigation of potential efficacy of existing drugs against this infection. Drug repurposing was done by performing virtual screening of already established drug molecules followed by 100 ns molecular dynamics simulations and molecular mechanics Poisson–Boltzmann surface area–based binding-energy calculation by targeting the SFTS L protein. On the basis of binding energy and protein–ligand interactions, top 10 promising hits were identified, showing stable binding with SFTS L protein. Further 100 ns atomistic MD simulation refined the hits from top 10 to top 4 with docking-based binding energy lesser than −8.0 kcal/mol toward the SFTS L protein and engaged in π–π interactions with pivotal amino acid residues. Various parameters and binding affinity of top 4 ligands towards L protein was computed. Ligand zaltoprofen exhibited best binding energy −220.095 kJ/mol. The present work is the first in silico study to assess bromfenac, cinchophen, elliptinium, and zaltoprofen; four promising hits against SFTS. Nonetheless, further proper biological evaluation is necessary to determine their efficacy against SFTS.