bluuebunny/crossref_metadata_2025_split huggingface dataset:
A20 promotes melanoma progression via the activation of Akt pathway
Authors: Ma Jinyuan , Wang Huina , Guo Sen , Yi Xiuli , Zhao Tao , Liu Yu , Shi Qiong , Gao Tianwen , Li Chunying , Guo Weinan 
Published: September 2020

AbstractMelanoma is the most life-threatening skin cancer with increasing incidence around the world. Although recent advances in targeted therapy and immunotherapy have brought revolutionary progress of the treatment outcome, the survival of patients with advanced melanoma remains unoptimistic, and metastatic melanoma is still an incurable disease. Therefore, to further understand the mechanism underlying melanoma pathogenesis could be helpful for developing novel therapeutic strategy. A20 is a crucial ubiquitin-editing enzyme implicated immunity regulation, inflammatory responses and cancer pathogenesis. Herein, we report that A20 played an oncogenic role in melanoma. We first found that the expression of A20 was significantly up-regulated in melanoma cell lines. Then, we showed that knockdown of A20 suppressed melanoma cell proliferation in vitro and melanoma growth in vivo through the regulation of cell-cycle progression. Moreover, A20 could potentiate the invasive and migratory capacities of melanoma cell in vitro and melanoma metastasis in vivo by promoting epithelial–mesenchymal transition (EMT). Mechanistically, we found that Akt activation mediated the oncogenic effect of A20 on melanoma development, with the involvement of glycolysis. What’s more, the up-regulation of A20 conferred the acquired resistance to Vemurafenib in BRAF-mutant melanoma. Taken together, we demonstrated that up-regulated A20 promoted melanoma progression via the activation of Akt pathway, and that A20 could be exploited as a potential therapeutic target for melanoma treatment.
A novel lncRNA LNC_000052 leads to the dysfunction of osteoporotic BMSCs via the miR-96-5p–PIK3R1 axis
Authors: Li Mingyang , Cong Rong , Yang Liyu , Yang Lei , Zhang Yiqi , Fu Qin 
Published: September 2020

AbstractBone marrow-derived mesenchymal stem cells (BMSCs) in postmenopausal osteoporosis models exhibit loss of viability and multipotency. Identification of the differentially expressed RNAs in osteoporotic BMSCs could reveal the mechanisms underlying BMSC dysfunction under physiological conditions, which might improve stem cell therapy and tissue regeneration. In this study, we performed high-throughput RNA sequencing and showed that the novel long non-coding RNA (lncRNA) LNC_000052 and its co-expressed mRNA PIK3R1 were upregulated in osteoporotic BMSCs. Knockdown of LNC_000052 could promote BMSC proliferation, migration, osteogenesis, and inhibit apoptosis via the PI3K/Akt signaling pathway. We found that both LNC_000052 and PIK3R1 shared a miRNA target, miR-96-5p, which was downregulated in osteoporotic BMSCs. Their binding sites were confirmed by dual-luciferase assays. Downregulation of miR-96-5p could restrain the effects of LNC_000052 knockdown while upregulation of miR-96-5p together with LNC_000052 knockdown could improve the therapeutic effects of BMSCs. In summary, the LNC_000052–miR-96-5p–PIK3R1 axis led to dysfunction of osteoporotic BMSCs and might be a novel therapeutic target for stem cell therapy and tissue regeneration.
Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth
Authors: Krivanek Jan , Soldatov Ruslan A. , Kastriti Maria Eleni , Chontorotzea Tatiana , Herdina Anna Nele , Petersen Julian , Szarowska Bara , Landova Marie , Matejova Veronika Kovar , Holla Lydie Izakovicova , Kuchler Ulrike , Zdrilic Ivana Vidovic , Vijaykumar Anushree , Balic Anamaria , Marangoni Pauline , Klein Ophir D. , Neves Vitor C. M. , Yianni Val , Sharpe Paul T. , Harkany Tibor , Metscher Brian D. , Bajénoff Marc , Mina Mina , Fried Kaj , Kharchenko Peter V. , Adameyko Igor 
Published: September 2020

AbstractUnderstanding cell types and mechanisms of dental growth is essential for reconstruction and engineering of teeth. Therefore, we investigated cellular composition of growing and non-growing mouse and human teeth. As a result, we report an unappreciated cellular complexity of the continuously-growing mouse incisor, which suggests a coherent model of cell dynamics enabling unarrested growth. This model relies on spatially-restricted stem, progenitor and differentiated populations in the epithelial and mesenchymal compartments underlying the coordinated expansion of two major branches of pulpal cells and diverse epithelial subtypes. Further comparisons of human and mouse teeth yield both parallelisms and differences in tissue heterogeneity and highlight the specifics behind growing and non-growing modes. Despite being similar at a coarse level, mouse and human teeth reveal molecular differences and species-specific cell subtypes suggesting possible evolutionary divergence. Overall, here we provide an atlas of human and mouse teeth with a focus on growth and differentiation.
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
Authors: Broom Aron , Rakotoharisoa Rojo V. , Thompson Michael C. , Zarifi Niayesh , Nguyen Erin , Mukhametzhanov Nurzhan , Liu Lin , Fraser James S. , Chica Roberto A. 
Published: September 2020

AbstractThe creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M−1s−1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M−1s−1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.
Effective interactions mediated between two permeable disks in an active fluid
Authors: Sebtosheikh Mahmoud , Naji Ali 
Published: September 2020

AbstractWe study steady-state properties of a bath of active Brownian particles (ABPs) in two dimensions in the presence of two fixed, permeable (hollow) disklike inclusions, whose interior and exterior regions can exhibit mismatching motility (self-propulsion) strengths for the ABPs. We show that such a discontinuous motility field strongly affects spatial distribution of ABPs and thus also the effective interaction mediated between the inclusions through the active bath. Such net interactions arise from soft interfacial repulsions between ABPs that sterically interact with and/or pass through permeable membranes assumed to enclose the inclusions. Both regimes of repulsion and attractive (albeit with different mechanisms) are reported and summarized in overall phase diagrams.
Epidemiology and risk factors for avascular necrosis in childhood systemic lupus erythematosus in a Taiwanese population
Authors: Tsai Hsin-Lin , Chang Jei-Wen , Lu Jen-Her , Liu Chin-Su 
Published: September 2020

AbstractChildhood-onset systemic lupus erythematosus (SLE) is associated with greater disease activity, more aggressive course, and high rates of organ damage. The prolonged use of corticosteroids in childhood SLE contributes to increased morbidity, including avascular necrosis (AVN). We conducted this retrospective study using claims data from the Taiwan National Health Insurance Research Database, enrolling 1,472 children with newly-diagnosed SLE between 2005 and 2013. The mean age at the diagnosis of SLE was 15.5 ± 3.3 years, and the female to male ratio was 6.2:1. Thirty-nine patients (2.6%) developed symptomatic AVN during a mean follow-up of 4.6 ± 2.5 years. In multivariate analysis, the risk of AVN was higher in the patients with a daily prednisolone dose between 7.5 mg and 30 mg (HR 7.435, 95% CI 2.882–19.178, p < 0.001) and over 30 mg (HR 9.366, 95% CI 2.225–39.418, p = 0.002) than in those with a dose ≤ 7.5 mg/day. In addition, AVN was inversely correlated with the use of hydroxychloroquine > 627 days (HR 0.335, 95% CI 0.162–0.694, p = 0.003). In conclusion, high daily doses of prednisolone were associated with a significant risk of AVN, whereas the use of hydroxychloroquine > 627 days conferred an advantage. We suggest that the judicious use of corticosteroids combined with hydroxychloroquine might be a promising preventive strategy for AVN.
Optimization of human papillomavirus-based pseudovirus techniques for efficient gene transfer
Authors: Gilson Timra D. , Gibson Ryan T. , Androphy Elliot J. 
Published: September 2020

AbstractHuman papillomavirus (HPV) L1 and L2 capsid proteins self-assemble into virions capable of efficiently packaging either its 8 kilobase genome or non-viral DNA. The ability of HPV capsids to package non-viral DNA makes these a useful tool for delivering plasmids to study proteins of interest in a variety of cell types. We describe optimization of current methods and present new protocols for using HPV capsids to deliver non-viral DNA thereby providing an alternative to DNA transfection. Using keratinocyte generated extracellular matrices can enhance infection efficiency in keratinocytes, hepatocytes and neuronal cells. Furthermore, we describe a suspension-based efficient technique for infecting different cell types.
Whitefly genomes contain ribotoxin coding genes acquired from plants
Authors: Lapadula Walter J. , Mascotti María L. , Juri Ayub Maximiliano 
Published: September 2020

AbstractRibosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and bacteria. Previously, we have described for the first time RIP genes in mosquitoes belonging to the Culicidae family. We showed that these genes are derived from a single event of horizontal gene transfer (HGT) from a prokaryotic donor. Mosquito RIP genes are evolving under purifying selection, strongly suggesting that these toxins have acquired a functional role. In this work, we show the existence of two RIP encoding genes in the genome of the whitefly Bemisia tabaci, a hemiptera species belonging to the Aleyrodidae family distantly related to mosquitoes. Contamination artifacts were ruled out analyzing three independent B. tabaci genome databases. In contrast to mosquito RIPs, whitefly genes harbor introns and according to transcriptomic evidence are transcribed and spliced. Phylogeny and the taxonomic distribution strongly support that whitefly RIP genes are derived from an independent HGT event from a plant source. These results, along with our previous description of RIPs in Diptera, suggest that the acquired genes are functional in these insects and confer some fitness advantage.
Animated virtual characters to explore audio-visual speech in controlled and naturalistic environments
Authors: Thézé Raphaël , Gadiri Mehdi Ali , Albert Louis , Provost Antoine , Giraud Anne-Lise , Mégevand Pierre 
Published: September 2020

AbstractNatural speech is processed in the brain as a mixture of auditory and visual features. An example of the importance of visual speech is the McGurk effect and related perceptual illusions that result from mismatching auditory and visual syllables. Although the McGurk effect has widely been applied to the exploration of audio-visual speech processing, it relies on isolated syllables, which severely limits the conclusions that can be drawn from the paradigm. In addition, the extreme variability and the quality of the stimuli usually employed prevents comparability across studies. To overcome these limitations, we present an innovative methodology using 3D virtual characters with realistic lip movements synchronized on computer-synthesized speech. We used commercially accessible and affordable tools to facilitate reproducibility and comparability, and the set-up was validated on 24 participants performing a perception task. Within complete and meaningful French sentences, we paired a labiodental fricative viseme (i.e. /v/) with a bilabial occlusive phoneme (i.e. /b/). This audiovisual mismatch is known to induce the illusion of hearing /v/ in a proportion of trials. We tested the rate of the illusion while varying the magnitude of background noise and audiovisual lag. Overall, the effect was observed in 40% of trials. The proportion rose to about 50% with added background noise and up to 66% when controlling for phonetic features. Our results conclusively demonstrate that computer-generated speech stimuli are judicious, and that they can supplement natural speech with higher control over stimulus timing and content.
Pseudo-Darwinian evolution of physical flows in complex networks
Authors: Berthelot Geoffroy , Tupikina Liubov , Kang Min-Yeong , Sapoval Bernard , Grebenkov Denis S. 
Published: September 2020

AbstractThe evolution of complex transport networks is investigated under three strategies of link removal: random, intentional attack and “Pseudo-Darwinian” strategy. At each evolution step and regarding the selected strategy, one removes either a randomly chosen link, or the link carrying the strongest flux, or the link with the weakest flux, respectively. We study how the network structure and the total flux between randomly chosen source and drain nodes evolve. We discover a universal power-law decrease of the total flux, followed by an abrupt transport collapse. The time of collapse is shown to be determined by the average number of links per node in the initial network, highlighting the importance of this network property for ensuring safe and robust transport against random failures, intentional attacks and maintenance cost optimizations.
Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP
Authors: Dominguez-Martin Maria Agustina , Hammel Michal , Gupta Sayan , Lechno-Yossef Sigal , Sutter Markus , Rosenberg Daniel J. , Chen Yan , Petzold Christopher J. , Ralston Corie Y. , Polívka Tomáš , Kerfeld Cheryl A. 
Published: September 2020

AbstractThe Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.
Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes
Authors: Gerashchenko Maxim V. , Nesterchuk Mikhail V. , Smekalova Elena M. , Paulo Joao A. , Kowalski Piotr S. , Akulich Kseniya A. , Bogorad Roman , Dmitriev Sergey E. , Gygi Steven , Zatsepin Timofei , Anderson Daniel G. , Gladyshev Vadim N. , Koteliansky Victor E. 
Published: September 2020

AbstractDue to breakthroughs in RNAi and genome editing methods in the past decade, it is now easier than ever to study fine details of protein synthesis in animal models. However, most of our understanding of translation comes from unicellular organisms and cultured mammalian cells. In this study, we demonstrate the feasibility of perturbing protein synthesis in a mouse liver by targeting translation elongation factor 2 (eEF2) with RNAi. We were able to achieve over 90% knockdown efficacy and maintain it for 2 weeks effectively slowing down the rate of translation elongation. As the total protein yield declined, both proteomics and ribosome profiling assays showed robust translational upregulation of ribosomal proteins relative to other proteins. Although all these genes bear the TOP regulatory motif, the branch of the mTOR pathway responsible for translation regulation was not activated. Paradoxically, coordinated translational upregulation of ribosomal proteins only occurred in the liver but not in murine cell culture. Thus, the upregulation of ribosomal transcripts likely occurred via passive mTOR-independent mechanisms. Impaired elongation sequesters ribosomes on mRNA and creates a shortage of free ribosomes. This leads to preferential translation of transcripts with high initiation rates such as ribosomal proteins. Furthermore, severe eEF2 shortage reduces the negative impact of positively charged amino acids frequent in ribosomal proteins on ribosome progression.
Roles of the Tol-Pal system in the Type III secretion system and flagella-mediated virulence in enterohemorrhagic Escherichia coli
Authors: Hirakawa Hidetada , Suzue Kazutomo , Takita Ayako , Awazu Chikako , Kurushima Jun , Tomita Haruyoshi 
Published: September 2020

AbstractThe Tol-Pal system is a protein complex that is highly conserved in many gram-negative bacteria. We show here that the Tol-Pal system is associated with the enteric pathogenesis of enterohemorrhagic E. coli (EHEC). Deletion of tolB, which is required for the Tol-Pal system decreased motility, secretion of the Type III secretion system proteins EspA/B, and the ability of bacteria to adhere to and to form attaching and effacing (A/E) lesions in host cells, but the expression level of LEE genes, including espA/B that encode Type III secretion system proteins were not affected. The Citrobacter rodentium, tolB mutant, that is traditionally used to estimate Type III secretion system associated virulence in mice did not cause lethality in mice while it induced anti-bacterial immunity. We also found that the pal mutant, which lacks activity of the Tol-Pal system, exhibited lower motility and EspA/B secretion than the wild-type parent. These combined results indicate that the Tol-Pal system contributes to the virulence of EHEC associated with the Type III secretion system and flagellar activity for infection at enteric sites. This finding provides evidence that the Tol-Pal system may be an effective target for the treatment of infectious diseases caused by pathogenic E. coli.
Multiplex enzyme activity imaging by MALDI-IMS of substrate library conversions
Authors: Klein Oliver , Haeckel Akvile , Reimer Ulf , Nebrich Grit , Schellenberger Eyk 
Published: September 2020

AbstractEnzymes are fundamental to biological processes and involved in most pathologies. Here we demonstrate the concept of simultaneously mapping multiple enzyme activities (EA) by applying enzyme substrate libraries to tissue sections and analyzing their conversion by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). To that end, we spray-applied a solution of 20 naturally derived peptides that are known substrates for proteases, kinases, and phosphatases to zinc-fixed paraffin tissue sections of mouse kidneys. After enzyme conversion for 5 to 120 min at 37 °C and matrix application, the tissue sections were imaged by MALDI-IMS. We could image incubation time-dependently 16 of the applied substrates with differing signal intensities and 12 masses of expected products. Utilizing inherent enzyme amplification, EA-IMS can become a powerful tool to locally study multiple, potentially even lowly expressed, enzyme activities, networks, and their pharmaceutical modulation. Differences in the substrate detectability highlight the need for future optimizations.
Complex genetic encoding of the hepatitis B virus on-drug persistence
Authors: Thai Hong , Lara James , Xu Xiaojun , Kitrinos Kathryn , Gaggar Anuj , Chan Henry Lik Yuen , Xia Guo-liang , Ganova-Raeva Lilia , Khudyakov Yury 
Published: September 2020

AbstractTenofovir disoproxil fumarate (TDF) is one of the nucleotide analogs capable of inhibiting the reverse transcriptase (RT) activity of HIV and hepatitis B virus (HBV). There is no known HBV resistance to TDF. However, detectable variation in duration of HBV persistence in patients on TDF therapy suggests the existence of genetic mechanisms of on-drug persistence that reduce TDF efficacy for some HBV strains without affording actual resistance. Here, the whole genome of intra-host HBV variants (N = 1,288) was sequenced from patients with rapid (RR, N = 5) and slow response (SR, N = 5) to TDF. Association of HBV genomic and protein polymorphic sites to RR and SR was assessed using phylogenetic analysis and Bayesian network methods. We show that, in difference to resistance to nucleotide analogs, which is mainly associated with few specific mutations in RT, the HBV on-TDF persistence is defined by genetic variations across the entire HBV genome. Analysis of the inferred 3D-structures indicates no difference in affinity of TDF binding by RT encoded by intra-host HBV variants that rapidly decline or persist in presence of TDF. This finding suggests that effectiveness of TDF recognition and binding does not contribute significantly to on-drug persistence. Differences in patterns of genetic associations to TDF response between HBV genotypes B and C and lack of a single pattern of mutations among intra-host variants sensitive to TDF indicate a complex genetic encoding of the trait. We hypothesize that there are many genetic mechanisms of on-drug persistence, which are differentially available to HBV strains. These pervasive mechanisms are insufficient to prevent viral inhibition completely but may contribute significantly to robustness of actual resistance. On-drug persistence may reduce the overall effectiveness of therapy and should be considered for development of more potent drugs.