bluuebunny/crossref_metadata_2025 huggingface dataset:
AFF4 regulates osteogenic differentiation of human dental follicle cells
Authors: Xiao Qingyue , Zhang Yuning , Qi Xingying , Chen Yaqian , Sheng Rui , Xu Ruoshi , Yuan Quan , Zhou Chenchen
Published: June 2020

As a member of the AFF (AF4/FMR2) family, AFF4 is a transcription elongation factor that is a component of the super elongation complex. AFF4 serves as a scaffolding protein that connects transcription factors and promotes gene transcription through elongation and chromatin remodelling. Here, we investigated the effect of AFF4 on human dental follicle cells (DFCs) in osteogenic differentiation. In this study, we found that small interfering RNA-mediated depletion ofAFF4resulted in decreased alkaline phosphatase (ALP) activity and impaired mineralization. In addition, the expression of osteogenic-related genes (DLX5,SP7,RUNX2andBGLAP) was significantly downregulated. In contrast, lentivirus-mediated overexpression ofAFF4significantly enhanced the osteogenic potential of human DFCs. Mechanistically, we found that both the mRNA and protein levels of ALKBH1, a critical regulator of epigenetics, changed in accordance with AFF4 expression levels. Overexpression ofALKBH1inAFF4-depleted DFCs partially rescued the impairment of osteogenic differentiation. Our data indicated that AFF4 promoted the osteogenic differentiation of DFCs by upregulating the transcription ofALKBH1.
Dynamic conjugate F-SHARP microscopy
Authors: Papadopoulos Ioannis N. , Jouhanneau Jean-Sebastien , Takahashi Naoya , Kaplan David , Larkum Matthew , Poulet James , Judkewitz Benjamin
Published: June 2020

Optical microscopy is an indispensable tool in biomedical sciences, but its reach in deep tissues is limited due to aberrations and scattering. This problem can be overcome by wavefront-shaping techniques, albeit at limited fields of view (FOVs). Inspired by astronomical imaging, conjugate wavefront shaping can lead to an increased field of view in microscopy, but this correction is limited to a set depth and cannot be dynamically adapted. Here, we present a conjugate wavefront-shaping scheme based on focus scanning holographic aberration probing (F-SHARP). We combine it with a compact implementation that can be readily adapted to a variety of commercial and home-built two-photon microscopes. We demonstrate the power of the method by imaging with high resolution over extended FOV (>80 µm) deeper than 400 μm inside a mouse brain through a thinned skull.
Action mechanisms and research methods of tRNA-derived small RNAs
Authors: Xie Yaoyao , Yao Lipeng , Yu Xiuchong , Ruan Yao , Li Zhe , Guo Junming
Published: June 2020

tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.
CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer
Authors: Lin Jian-xian , Yoon Changhwan , Li Ping , Ryeom Sandra W. , Cho Soo-Jeong , Zheng Chao-hui , Xie Jian-wei , Wang Jian-bin , Lu Jun , Chen Qi-yue , Yoon Sam S. , Huang Chang-ming
Published: June 2020

Background

Toward identifying new strategies to target gastric cancer stem-like cells (CSCs), we evaluated the function of the tumour suppressor CDK5 regulatory subunit-associated protein 3 (CDK5RAP3) in gastric CSC maintenance.

Methods

We examined the expression of CDK5RAP3 and CD44 in gastric cancer patients. The function and mechanisms of CDK5RAP3 were checked in human and mouse gastric cancer cell lines and in mouse xenograft.

Results

We show that CDK5RAP3 is weakly expressed in gastric CSCs and is negatively correlated with the gastric CSC marker CD44. CDK5RAP3 overexpression decreased expression of CSC markers, spheroid formation, invasion and migration, and reversed chemoresistance in gastric CSCs in vitro and vivo. CDK5RAP3 expression was found to be regulated by extracellular-related kinase (ERK) signalling. ERK inhibitors decreased spheroid formation, migration and invasion, and the expression of epithelial-to-mesenchymal transition (EMT)-related proteins in both GA cells and organoids derived from a genetically engineered mouse model of GA. Finally, CDK5RAP3 expression was associated with reduced lymph-node metastasis and better prognosis, even in the presence of high expression of the EMT transcription factor Snail, among patients with CD44-positive GA.

Conclusions

Our results demonstrate that CDK5RAP3 is suppressed by ERK signalling and negatively regulates the self-renewal and EMT of gastric CSCs.
Paracrine SPARC signaling dysregulates alveolar epithelial barrier integrity and function in lung fibrosis
Authors: Conforti Franco , Ridley Robert , Brereton Christopher , Alzetani Aiman , Johnson Benjamin , Marshall Ben G. , Fletcher Sophie V. , Ottensmeier Christian H. , Richeldi Luca , Skipp Paul , Wang Yihua , Jones Mark G. , Davies Donna E.
Published: June 2020

Idiopathic pulmonary fibrosis (IPF) is a chronic scarring disease in which aging, environmental exposure(s) and genetic susceptibility have been implicated in disease pathogenesis, however, the causes and mechanisms of the progressive fibrotic cascade are still poorly understood. As epithelial–mesenchymal interactions are essential for normal wound healing, through human 2D and 3D in vitro studies, we tested the hypothesis that IPF fibroblasts (IPFFs) dysregulate alveolar epithelial homeostasis. Conditioned media from IPFFs exaggerated the wound-healing response of primary human Type II alveolar epithelial cells (AECs). Furthermore, AECs co-cultured with IPFFs exhibited irregular epithelialization compared with those co-cultured with control fibroblasts (NHLFs) or AECs alone, suggesting that epithelial homeostasis is dysregulated in IPF as a consequence of the abnormal secretory phenotype of IPFFs. Secretome analysis of IPFF conditioned media and functional studies identified the matricellular protein, SPARC, as a key mediator in the epithelial–mesenchymal paracrine signaling, with increased secretion of SPARC by IPFFs promoting persistent activation of alveolar epithelium via an integrin/focal adhesion/cellular-junction axis resulting in disruption of epithelial barrier integrity and increased macromolecular permeability. These findings suggest that in IPF fibroblast paracrine signaling promotes persistent alveolar epithelial activation, so preventing normal epithelial repair responses and restoration of tissue homeostasis. Furthermore, they identify SPARC-mediated paracrine signaling as a potential therapeutic target to promote the restoration of lung epithelial homoestasis in IPF patients.
Regulation of flowering time in chrysanthemum by the R2R3 MYB transcription factor CmMYB2 is associated with changes in gibberellin metabolism
Authors: Zhu Lu , Guan Yunxiao , Liu Yanan , Zhang Zhaohe , Jaffar Muhammad Abuzar , Song Aiping , Chen Sumei , Jiang Jiafu , Chen Fadi
Published: June 2020

The switch from vegetative growth to reproductive growth is a key event in the development of a plant. Here, the product of the chrysanthemum geneCmMYB2, an R2R3 MYB transcription factor that is localized in the nucleus, was shown to be a component of the switching mechanism. Plants engineered to overexpressCmMYB2flowered earlier than did wild-type plants, while those in whichCmMYB2was suppressed flowered later. In both the overexpression and RNAi knockdown plants, a number of genes encoding proteins involved in gibberellin synthesis or signaling, as well as in the response to photoperiod, were transcribed at a level that differed from that in the wild type. Both yeast two-hybrid and bimolecular fluorescence complementation assays revealed that CmMYB2 interacts with CmBBX24, a zinc-finger transcription factor known to regulate flowering by its influence on gibberellin synthesis.
Molecular identification of the key starch branching enzyme-encoding gene SBE2.3 and its interacting transcription factors in banana fruits
Authors: Miao Hongxia , Sun Peiguang , Liu Qing , Liu Juhua , Jia Caihong , Zhao Dongfang , Xu Biyu , Jin Zhiqiang
Published: June 2020

Starch branching enzyme (SBE) has rarely been studied in common starchy banana fruits. For the first time, we report here the molecular characterization of seven SBE (MaSBE) and six SBE (MbSBE) genes in the banana A- and B-genomes, respectively, which could be classified into three distinct subfamilies according to genome-wide identification. Systematic transcriptomic analysis revealed that six MaSBEs and six MbSBEs were expressed in the developing banana fruits of two different genotypes, BaXi Jiao (BX, AAA) and Fen Jiao (FJ, AAB), among which MaSBE2.3 and MbSBE2.3 were highly expressed. Transient silencing of MaSBE2.3 expression in banana fruit discs led to a significant decrease in its transcription, which coincides with significant reductions in total starch and amylopectin contents compared to those of empty vector controls. The suggested functional role of MaSBE2.3 in banana fruit development was corroborated by its transient overexpression in banana fruit discs, which led to significant enhancements in total starch and amylopectin contents. A number of transcription factors, including three auxin response factors (ARF2/12/24) and two MYBs (MYB3/308), that interact with the MaSBE2.3 promoter were identified by yeast one-hybrid library assays. Among these ARFs and MYBs, MaARF2/MaMYB308 and MaARF12/MaARF24/MaMYB3 were demonstrated via a luciferase reporter system to upregulate and downregulate the expression of MaSBE2.3, respectively.
Functional analysis of a novel C-glycosyltransferase in the orchid Dendrobium catenatum
Authors: Ren Zhiyao , Ji Xiaoyu , Jiao Zhenbin , Luo Yingyi , Zhang Guo-Qiang , Tao Shengchang , Lei Zhouxi , Zhang Jing , Wang Yuchen , Liu Zhong-Jian , Wei Gang
Published: June 2020

Flavonoids, which are a diverse class of phytonutrients, are used by organisms to respond to nearly all abiotic stresses and are beneficial for human health. Glycosyltransferase, used during the last step of flavonoid biosynthesis, is important in flavonoid enrichment. However, little is known about glycosyltransferase in the orchid Dendrobium catenatum (D. officinale). In this study, we isolated a novel C-glycosyltransferase (designated DcaCGT) from the orchid D. catenatum by identifying and analyzing 82 putative genes in the GT1 family. DcaCGT could specifically catalyze not only di-C-glycosylation but also O-glycosylation. Apart from the normal function of catalyzing 2-hydroxynaringenin and phloretin to the respective di-C-glycosides, DcaCGT also catalyzes apigenin to cosmosiin. Targeted metabolic profiling of the substrates (2-hydroxynaringenin, phloretin, and apigenin) and products (vitexin, isovitexin, vicenin-2, nothofagin, 3’,5’-di-C-glucosylphloretin, and cosmosiin) in different tissues showed that vicenin-2 was the most abundant product of this novel enzyme. Cosmosiin was detected in flowers and flower buds. We also established that DcaCGT functions expanded throughout the evolution of D. catenatum. Residual OGT activity may help D. catenatum resist drought stress. Our study illustrates the function, origin, and differentiation of DcaCGT and provides insights into glycosylation and molecular propagation processes, which can be used to improve the production of flavonoids by the cultivated medicinal plant D. catenatum.
Genome-wide identification of microRNAs involved in the regulation of fruit ripening and climacteric stages in melon (Cucumis melo)
Authors: Bai Selinge , Tian Yunyun , Tan Chao , Bai Shunbuer , Hao Jinfeng , Hasi Agula
Published: June 2020

Fruit ripening is influenced by multiple plant hormones and the regulation of genes. However, studies on posttranscriptional regulators (e.g., miRNAs) of fruit growth and ripening are limited. We used miRNA sequencing and degradome methods to identify miRNAs and their target genes in melon (Cucumis melo cv. Hetao melon). A total of 61 conserved miRNAs and 36 novel miRNAs were identified from fruit growth, ripening, climacteric, and postclimacteric developmental stage samples, of which 32 conserved miRNAs were differentially expressed between developmental stage samples. Sixty-two target genes of 43 conserved miRNAs and 1 novel miRNA were identified from degradome sequencing. To further investigate miRNA influencing fruit ripening, transgenic melon plants overexpressing pre-cme-miR393 (cme-miR393-OE) were generated and characterized. The results showed that fruit ripening was delayed in cme-miR393-OE transgenic lines compared to nontransgenic fruits. The target of cme-miR393 was also identified, and the expression of CmAFB2 was repressed in transgenic plants. These results provide evidence that miRNA regulates melon fruit ripening and provide potential targets to improve the horticultural traits of melon fruit.
Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia
Authors: Riaz Summaira , Menéndez Cristina M. , Tenscher Alan , Pap Daniel , Walker M. Andrew
Published: June 2020

Cultivated grapevines (Vitis vinifera) lack resistance to powdery mildew (PM) with few exceptions. Resistance to this pathogen within V. vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions. Other PM-resistant cultivated varieties and accessions of the wild ancestor V. vinifera subsp. sylvestris were soon identified raising questions regarding the origin of the resistance. In this study, F1 breeding populations were developed with a PM susceptible V. vinifera subsp. vinifera breeding line and a PM-resistant subsp. sylvestris accession. Genotyping was carried out with five Ren1 locus linked SSR markers. A PM resistance locus explaining up to 96% of the phenotypic variation was identified in the same genomic position, where the Ren1 locus was previously reported. New SSR marker alleles linked with the resistance locus were identified. We report results of PM resistance in multiple accessions of subsp. sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia. A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia, Armenia, and Azerbaijan were resistant to PM. Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM. Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes, which are only possible via recombination events occurring over a long time period. Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms. Variable levels of PM resistance among the tested accessions were also observed. These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought, giving the wild progenitor V. vinifera subsp. sylvestris time to coevolve with and develop resistance to this pathogen.
Author Correction: Therapeutic potential of KLF2-induced exosomal microRNAs in pulmonary hypertension
Authors: Sindi Hebah A. , Russomanno Giusy , Satta Sandro , Abdul-Salam Vahitha B. , Jo Kyeong Beom , Qazi-Chaudhry Basma , Ainscough Alexander J. , Szulcek Robert , Bogaard Harm Jan , Morgan Claire C. , Pullamsetti Soni S. , Alzaydi Mai M. , Rhodes Christopher J. , Piva Roberto , Eichstaedt Christina A. , Grünig Ekkehard , Wilkins Martin R. , Wojciak-Stothard Beata
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Embedding physics domain knowledge into a Bayesian network enables layer-by-layer process innovation for photovoltaics
Authors: Ren Zekun , Oviedo Felipe , Thway Maung , Tian Siyu I. P. , Wang Yue , Xue Hansong , Perea Jose Dario , Layurova Mariya , Heumueller Thomas , Birgersson Erik , Aberle Armin G. , Brabec Christoph J. , Stangl Rolf , Li Qianxiao , Sun Shijing , Lin Fen , Peters Ian Marius , Buonassisi Tonio
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Holocene global mean surface temperature, a multi-method reconstruction approach
Authors: Kaufman Darrell , McKay Nicholas , Routson Cody , Erb Michael , Dätwyler Christoph , Sommer Philipp S. , Heiri Oliver , Davis Basil
Published: June 2020

An extensive new multi-proxy database of paleo-temperature time series (Temperature 12k) enables a more robust analysis of global mean surface temperature (GMST) and associated uncertainties than was previously available. We applied five different statistical methods to reconstruct the GMST of the past 12,000 years (Holocene). Each method used different approaches to averaging the globally distributed time series and to characterizing various sources of uncertainty, including proxy temperature, chronology and methodological choices. The results were aggregated to generate a multi-method ensemble of plausible GMST and latitudinal-zone temperature reconstructions with a realistic range of uncertainties. The warmest 200-year-long interval took place around 6500 years ago when GMST was 0.7 °C (0.3, 1.8) warmer than the 19th Century (median, 5th, 95th percentiles). Following the Holocene global thermal maximum, GMST cooled at an average rate −0.08 °C per 1000 years (−0.24, −0.05). The multi-method ensembles and the code used to generate them highlight the utility of the Temperature 12k database, and they are now available for future use by studies aimed at understanding Holocene evolution of the Earth system.
Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity
Authors: Bulut Haydar , Hattori Shin-ichiro , Aoki-Ogata Hiromi , Hayashi Hironori , Das Debananda , Aoki Manabu , Davis David A. , Rao Kalapala Venkateswara , Nyalapatla Prasanth R. , Ghosh Arun K. , Mitsuya Hiroaki
Published: June 2020

HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. However, HIV-1 often acquires resistance to PIs. Here, seven novel PIs were synthesized, by introducing single atom changes such as an exchange of a sulfur to an oxygen, scission of a single bond in P2′-cyclopropylaminobenzothiazole (or -oxazole), and/or P1-benzene ring with fluorine scan of mono- or bis-fluorine atoms around DRV’s scaffold. X-ray structural analyses of the PIs complexed with wild-type Protease (PRWT) and highly-multi-PI-resistance-associated PRDRVRP51 revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2′-subsite. Furthermore, these PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Our work provides the basis for developing novel PIs with high potency against PI-resistant HIV-1 variants with a high genetic barrier.
Cholecystectomy - a potential selection bias in studies assessing the metabolic effects of bariatric surgeries
Authors: Machado Natasha Mendonça , Cardinelli Camila de Siqueira , Shen Tong , Santo Marco Aurélio , Torrinhas Raquel Susana , Waitzberg Dan Linetzky
Published: June 2020

Bile acids (BAs) are key mediators of the glycemic control after bariatric surgeries. Cholecystectomy modifies the kinetics of BAs, and whether this procedure influences the BAs pool and its metabolic response to bariatric surgeries is not known. We used targeted and untargeted metabolomics to assess whether cholecystectomy influenced plasma and fecal BAs fluctuations and the systemic metabolomic profile after Roux-en-Y gastric bypass (RYGB). Women with obesity and type 2 diabetes were included. Sample collections and clinical evaluations were performed before and 3 months after RYGB. RYGB influenced 9 fecal and 3 plasma BAs in patients with cholecystectomy (p ≤ 0.05). Comparisons between patients with and without cholecystectomy revealed different concentrations of 4 fecal and 5 plasma BAs (p ≤ 0.05). Cholecystectomy impacted the global metabolomics responses to RYGB, and patients who underwent the gallbladder removal also lacked some significant improvements in clinical markers, primarily the lipid profile. By affecting the BAs concentrations, cholecystectomy seems to alter the systemic metabolic response to RYGB. Therefore, cholecystectomy may act as a bias in assessments of the metabolic effects of bariatric surgeries and their relationships with clinical outcomes.
Quantifying the spreading resistance of an anisotropic thin film conductor
Authors: Seki Kazuhiko , Kubo Toshitaka , Ye Nan , Shimizu Tetsuo
Published: June 2020

Recently, highly anisotropic conductors, such as multilayer graphene, have been attracting much attention. The local resistivity can be determined by measuring the contact resistance; however, the theoretical expressions of contact resistance have been developed for isotropic slabs but have not been well developed for highly anisotropic film conductors. We obtain theoretical expressions of the spreading resistance below the circular contact for a highly anisotropic film on a bulk slab. The film spreading resistance of isotropic conductors deviates from the bulk spreading resistance when the film thickness is smaller than the contact radius. Nevertheless, the spreading resistance of anisotropic conducting films can be approximated by that of the bulk slabs even when the film thickness is smaller than the contact radius if the in-plane electrical conductivity is larger than the out-of-plane electrical conductivity. Owing to the high in-plane conductivity, the spreading resistance of anisotropic bulk conductors can be lowered from that predicted by the Holm’s equation obtained using the out-of-plane conductivity and the contact radius. We show that these characteristics are beneficial to use the highly anisotropic film as a cover layer when the in-plane conductivity of the film is high and the conductivity of the base slab is low.
Vesicular stomatitis virus nucleocapsids diffuse through cytoplasm by hopping from trap to trap in random directions
Authors: Holzwarth George , Bhandari Arnav , Tommervik Lucas , Macosko Jed C. , Ornelles David A. , Lyles Douglas S.
Published: June 2020

Within 2–6 hours after infection by vesicular stomatitis virus (VSV), newly assembled VSV particles are released from the surface of infected cells. In that time, viral ribonucleoprotein (RNP) particles (nucleocapsids) travel from their initial sites of synthesis near the nucleus to the edge of the cell, a distance of 5–10 μm. The hydrodynamic radius of RNP particles (86 nm) precludes simple diffusion through the mesh of cytoskeletal fibers. To reveal the relative importance of different transport mechanisms, movement of GFP-labeled RNP particles in live A549 cells was recorded within 3 to 4 h postinfection at 100 frames/s by fluorescence video microscopy. Analysis of more than 200 RNP particle tracks by Bayesian pattern recognition software found that 3% of particles showed rapid, directional motion at about 1 μm/s, as previously reported. 97% of the RNP particles jiggled within a small, approximately circular area with Gaussian width σ = 0.06 μm. Motion within such “traps” was not directional. Particles stayed in traps for approximately 1 s, then hopped to adjacent traps whose centers were displaced by approximately 0.17 μm. Because hopping occurred much more frequently than directional motion, overall transport of RNP particles was dominated by hopping over the time interval of these experiments.
TGF-β induced EMT and stemness characteristics are associated with epigenetic regulation in lung cancer
Authors: Kim Bit Na , Ahn Dong Hyuck , Kang Nahyeon , Yeo Chang Dong , Kim Young Kyoon , Lee Kyo Young , Kim Tae-Jung , Lee Sug Hyung , Park Mi Sun , Yim Hyeon Woo , Park Jong Y. , Park Chan Kwon , Kim Seung Joon
Published: June 2020

Transforming growth factor-β (TGF-β) promotes tumor invasion and metastasis by inducing epithelial-mesenchymal transition (EMT). EMT is often related with acquisition of stemness characteristics. The objective of this study was to determine whether EMT and stemness characteristics induced by TGF-β might be associated with epigenetic regulation in lung cancer. A human normal lung epithelial cell line and four lung cancer cell lines were treated with TGF-β. Transcriptome analysis of BEAS-2B and A549 cells incubated with TGF-β were analyzed through next-generation sequencing (NGS). Western blotting was carried out to investigate expression levels of epithelial and mesenchymal markers. Wound healing and Matrigel invasion assay, sphere formation assay, and in vivo mice tumor model were performed to evaluate functional characteristics of EMT and stemness acquisition. To investigate whether activation of EMT and stem cell markers might be involved in epigenetic regulation of lung cancer, experiment using a DNA methyltransferase inhibitor (5-azacytidine, AZA), methylation-specific PCR (MSP) and bisulfite sequencing were performed. NGS revealed changes in expression levels of EMT markers (E-cadherin, N-cadherin, fibronectin, vimentin, slug and snail) and stem cell markers (CD44 and CD87) in both BEAS-2B and A549 cells. Functional analysis revealed increased migration, invasion, sphere formation, and tumor development in mice after TGF-β treatment. Expression of slug and CD87 genes was activated following treatment with AZA and TGF-β. MSP and bisulfite sequencing indicated DNA demethylation of slug and CD87 genes. These results suggest that TGF-β induced EMT and cancer stemness acquisition could be associated with activation of slug and CD87 gene by their promoter demethylation.
p32/C1QBP regulates OMA1-dependent proteolytic processing of OPA1 to maintain mitochondrial connectivity related to mitochondrial dysfunction and apoptosis
Authors: Noh Solhee , Phorl Sophors , Naskar Rema , Oeum Kakada , Seo Yuri , Kim Eunjung , Kweon Hee-Seok , Lee Joo-Yong
Published: June 2020

Mitochondria are dynamic organelles that undergo fusion and fission in response to various physiological and stress stimuli, which play key roles in diverse mitochondrial functions such as energy metabolism, intracellular signaling, and apoptosis. OPA1, a mitochondrial dynamin-like GTPase, is responsible for the inner membrane fusion of mitochondria, and the function of OPA1 is regulated by proteolytic cleavage in response to various metabolic stresses. Growing evidences highlighted the importance of mitochondrial adaptation in response to metabolic stimuli. Here, we demonstrated the role of p32/C1QBP in mitochondrial morphology by regulating OMA1-dependent proteolytic processing of OPA1. Genetic ablation of p32/C1QBP activates OMA1, cleaves OPA1, and leads mitochondrial fragmentation and swelling. The loss of p32/C1QBP decreased mitochondrial respiration and lipid utilization, sensitized cells to mitochondrial stress, and triggered a metabolic shift from oxidative phosphorylation to glycolysis, which were correlated with apoptosis in cancer cells and the inhibition of 3D-spheroid formation. These results suggest a unique regulation of cell physiology by mitochondria and provide a basis for a new therapeutic strategy for cancer.
miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome
Authors: Liu Yifan , Zhang Ming , Shan Yanju , Ji Gaige , Ju Xiaojun , Tu Yunjie , Sheng Zhongwei , Xie Jingfang , Zou Jianmin , Shu Jingting
Published: June 2020

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.
Maximum entropy approach to multivariate time series randomization
Authors: Marcaccioli Riccardo , Livan Giacomo
Published: June 2020

Natural and social multivariate systems are commonly studied through sets of simultaneous and time-spaced measurements of the observables that drive their dynamics, i.e., through sets of time series. Typically, this is done via hypothesis testing: the statistical properties of the empirical time series are tested against those expected under a suitable null hypothesis. This is a very challenging task in complex interacting systems, where statistical stability is often poor due to lack of stationarity and ergodicity. Here, we describe an unsupervised, data-driven framework to perform hypothesis testing in such situations. This consists of a statistical mechanical approach—analogous to the configuration model for networked systems—for ensembles of time series designed to preserve, on average, some of the statistical properties observed on an empirical set of time series. We showcase its possible applications with a case study on financial portfolio selection.
Enzyme-catalysed mineralisation experiment study to solidify desert sands
Authors: Miao Linchang , Wu Linyu , Sun Xiaohao
Published: June 2020

Sandstorms are meteorological phenomena common in arid and semi-arid regions and have been recognized severe natural disasters worldwide. The key problem is how to control and mitigate sandstorm natural disasters. This research aims to mitigate their development by improving surface stability and soil water retention properties through soil mineralization. The enzymatic induced carbonate precipitation (EICP) is proposed to solidify desert sands and form a hard crust layer on the surface of desert sands. In contrast to micro-induced carbonate precipitation commonly used at room temperatures, EICP had high production efficiency and productivity at a broader temperature range (10–70 °C ±) and significantly improves material water retention properties, which was more suitable to desert environment. Results demonstrate that the enzyme-catalysed mineralisation method can be better resistance to high winds as the number of spraying times increased.
Soil as an extended composite phenotype of the microbial metagenome
Authors: Neal Andrew L. , Bacq-Labreuil Aurélie , Zhang Xiaoxian , Clark Ian M. , Coleman Kevin , Mooney Sacha J. , Ritz Karl , Crawford John W.
Published: June 2020

We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air–water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.
Parkinsonian neurotoxicants impair the anti-inflammatory response induced by IL4 in glial cells: involvement of the CD200-CD200R1 ligand-receptor pair
Authors: Rabaneda-Lombarte Neus , Blasco-Agell Lucas , Serratosa Joan , Ferigle Laura , Saura Josep , Solà Carme
Published: June 2020

Exposure to pesticides such as rotenone is a risk factor for Parkinson’s disease. Dopaminergic neurons are especially sensitive to the toxicity of compounds that inhibit the mitochondrial respiratory chain such as rotenone and 1-methyl-4-phenylpyridinium (MPP+). However, there is scarce information on their effects on glia. To evaluate whether these neurotoxicants affect the immune response of glia, primary mouse mixed glial and microglial cultures were treated with interleukin (IL) 4 in the absence and presence of MPP+ or rotenone. Using qRTPCR or western blot, we determined the expression of anti-inflammatory markers, the CD200R1 microglial receptor and its ligand CD200, and genes regulating glycolysis and oxidative metabolism. ATP and lactate levels were additionally determined as an index of cell metabolism. Microglial phagocytosis was also evaluated. MPP+ and rotenone clearly abrogated the IL4-induced expression of anti-inflammatory markers in mixed glial cultures. CD200 and CD200R1 expression and microglia phagocytosis were also affected by the neurotoxicants. Changes in the mRNA expression of the molecules regulating glycolysis and oxidative metabolism, as well as in ATP levels and lactate release suggested that metabolic reprogramming in response to MPP+ and rotenone differs between microglial and mixed glial cultures. These findings support the hypothesis that parkinsonian neurotoxicants may impair brain immune response altering glial cell metabolism.
Beta-nerve growth factor stimulates spontaneous electrical activity of in vitro embryonic mouse GnRH neurons through a P75 mediated-mechanism
Authors: Pinet-Charvet Caroline , Fleurot Renaud , Derouin-Tochon Flavie , de Graaf Simon , Druart Xavier , Tsikis Guillaume , Taragnat Catherine , Teixeira-Gomes Ana-Paula , Labas Valérie , Moreau Thierry , Cayla Xavier , Duittoz Anne H
Published: June 2020

The control of ovulation helps guarantee the success of reproduction and as such, contributes to the fitness of a species. In mammals, two types of ovulation are observed: induced and spontaneous ovulation. Recent work on camelids, that are induced ovulators, highlighted the role of a factor present in seminal plasma, beta Nerve Growth Factor (β-NGF), as the factor that triggers ovulation in a GnRH dependent manner. In the present work, we characterized alpaca β-NGF (aβ-NGF) and its 3D structure and compared it with human recombinant β-NGF (hβ-NGF). We showed that the β-NGF enriched fraction of alpaca semen and the human recombinant protein, both stimulated spontaneous electrical activity of primary GnRH neurons derived from mouse embryonic olfactory placodes. This effect was dose-dependent and mediated by p75 receptor signaling. P75 receptors were found expressed in vitro by olfactory ensheathing cells (OEC) in close association with GnRH neurons and in vivo by tanycytes in close vicinity to GnRH fibers in adult mouse. Altogether, these results suggested that β-NGF induced ovulation through an increase in GnRH secretion provoked by a glial dependent P75 mediated mechanism.
Effects of novel non-thermal atmospheric plasma treatment of titanium on physical and biological improvements and in vivo osseointegration in rats
Authors: Zheng Zheng , Ao Xiaogang , Xie Peng , Wu Jie , Dong Yuqing , Yu Deping , Wang Jian , Zhu Zhimin , Xu Hockin H. K. , Chen Wenchuan
Published: June 2020

Titanium (Ti) has achieved extensive applications due to its excellent biocompatibility and mechanical properties. Plasma can enhance surface hydrophilia of Ti with decreased carbon contamination. The traditional conditions using a single gas plasma was for longer treatment time and more prone to being contaminated. We designed and developed novel and universal apparatus and methods with a special clamping device of non-thermal atmospheric plasma (NTAP) treatment using mixed gas for Ti surface activation. We systematically and quantitatively investigated the effective effects of NTAP-Ti. The surface water contact angle decreased by 100%, the carbon content decreased by 80% and oxygen content increased by 50% in the novel NTAP-Ti surfaces. NTAP treatment accelerated the attachment, spread, proliferation, osteogenic differentiation and mineralization of MC3T3-E1 mouse preosteoblasts in vitro. The percentage of bone-to-implant contact increased by 25–40%, and the osteoclasts and bone resorption were suppressed by 50% in NTAP-Ti in vivo. In conclusion, NTAP-Ti substantially enhanced the physical and biological effects and integration with bone. The novel and universal apparatus and methods with a special clamping device using gas mixtures are promising for implant activation by swiftly and effectively changing the Ti surface to a hydrophilic one to enhance dental and orthopedic applications.
Zebrafish (Danio rerio) physiological and behavioural responses to insect-based diets: a multidisciplinary approach
Authors: Zarantoniello Matteo , Randazzo Basilio , Gioacchini Giorgia , Truzzi Cristina , Giorgini Elisabetta , Riolo Paola , Gioia Giorgia , Bertolucci Cristiano , Osimani Andrea , Cardinaletti Gloriana , Lucon-Xiccato Tyrone , Milanović Vesna , Annibaldi Anna , Tulli Francesca , Notarstefano Valentina , Ruschioni Sara , Clementi Francesca , Olivotto Ike
Published: June 2020

Black Soldier Fly (BSF) meal is considered as an alternative, emerging and sustainable ingredient for aquafeed production. However, results on fish physiological responses are still fragmentary and often controversial, while no studies are available on fish behavior in response to these new diets. The present work represents the first comprehensive multidisciplinary study aimed to investigate zebrafish physiological and behavioural responses to BSF-based diets. Five experimental diets characterized by increasing inclusion levels (0, 25, 50, 75 and 100% respect to fish meal) of full fat BSF prepupae meal were tested during a 2-months feeding trial. Prepupae were cultured on coffee silverskin growth substrate enriched with a 10%Schizochytriumsp. to improve insects’ fatty acids profile. The responses of zebrafish were assayed through biometric, histological, gas chromatographic, microbiological, spectroscopic, molecular and behavioural analyses. Results evidenced that BSF-based diets affected fish fatty acid composition, while behavioural tests did not show differences among groups. Specifically, a 50% BSF inclusion level diet represented the best compromise between ingredient sustainability and proper fish growth and welfare. Fish fed with higher BSF inclusions (75 and 100%) showed hepatic steatosis, microbiota modification, higher lipid content, fatty acid modification and higher expression of immune response markers.
Cardiomyocyte-specific deletion of GCN5L1 in mice restricts mitochondrial protein hyperacetylation in response to a high fat diet
Authors: Thapa Dharendra , Manning Janet R. , Stoner Michael W. , Zhang Manling , Xie Bingxian , Scott Iain
Published: June 2020

Mitochondrial lysine acetylation regulates several metabolic pathways in cardiac cells. The current study investigated whether GCN5L1-mediated lysine acetylation regulates cardiac mitochondrial metabolic proteins in response to a high fat diet (HFD). GCN5L1 cardiac-specific knockout (cKO) mice showed significantly reduced mitochondrial protein acetylation following a HFD relative to wildtype (WT) mice. GCN5L1 cKO mice did not display any decrease in ex vivo cardiac workload in response to a HFD. In contrast, ex vivo cardiac function in HFD-fed WT mice dropped ~ 50% relative to low fat diet (LFD) fed controls. The acetylation status of electron transport chain Complex I protein NDUFB8 was significantly increased in WT mice fed a HFD, but remained unchanged in GCN5L1 cKO mice relative to LFD controls. Finally, we observed that inhibitory acetylation of superoxide dismutase 2 (SOD2) at K122 was increased in WT (but not cKO mice) on a HFD. This correlated with significantly increased cardiac lipid peroxidation in HFD-fed WT mice relative to GCN5L1 cKO animals under the same conditions. We conclude that increased GCN5L1 expression in response to a HFD promotes increased lysine acetylation, and that this may play a role in the development of reactive oxygen species (ROS) damage caused by nutrient excess.
Author Correction: Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention
Authors: Grembi Jessica A. , Nguyen Lan H. , Haggerty Thomas D. , Gardner Christopher D. , Holmes Susan P. , Parsonnet Julie
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins
Authors: Goutham Shyamili , Kumari Indu , Pally Dharma , Singh Alvina , Ghosh Sujasha , Akhter Yusuf , Bhat Ramray
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Graphene-MoS2 vertically anchored on an MXene-derived accordion-like TiO2/C skeleton: an ultrastable HER catalyst
Authors: Li Jian , Wen Zi , Hui Zhen Xin , Chen Zhi Wen , Yang Chun Cheng , Jiang Qing
Published: June 2020

An MXene-derived accordion-like TiO2/C substrate was fabricated for the first time and the as-fabricated rGO-MoS2/Acc-TiO2/C catalyst exhibited ultrahigh electrochemical stability in a strong acid electrolyte for the hydrogen evolution reaction.
Direct differentiation of whole blood for forensic serology analysis by thread spray mass spectrometry
Authors: Jackson Sierra , Frey Benjamin S. , Bates Maia N. , Swiner Devin J. , Badu-Tawiah Abraham K.
Published: June 2020

Direct analysis of whole blood on bloodstained textiles is achieved with thread spray mass spectrometry (MS).
Interactions between gold, thiol and As(iii) for colorimetric sensing
Authors: Duan Junling , Liu Biwu , Liu Juewen
Published: June 2020

Arsenite cannot crosslink glutathione-capped gold nanoparticles but a high concentration of arsenite can displace adsorbed glutathione, indicating that any two species from gold, thiol and arsenite can react.
A ratiometric fluorescent biosensor for the sensitive determination of α-glucosidase activity and acarbose based on N-doped carbon dots
Authors: Wang Mengjun , Wang Mengke , Zhang Feng , Su Xingguang
Published: June 2020

A ratiometric fluorescent biosensor for the determination of α-glucosidase and acarbose was constructed based on the N-CDs/PHQ-PEI system.
Europium chelate-labeled lateral flow assay for rapid and multiple detection of β-lactam antibiotics by the penicillin-binding protein
Authors: Li Xiaogang , Pan Zhifeng , Li Manyu , Jia Xinmiao , Zhang Suhan , Lin Hang , Liu Juntao , Ma Liangkun
Published: June 2020

A lateral flow assay for rapid and multiple detection of β-lactam antibiotics by the penicillin-binding protein was developed.
An accurate and ultrasensitive SERS sensor with Au–Se interface for bioimaging and in situ quantitation
Authors: Li Xiaoxiao , Duan Xiaoyan , Li Lu , Ye Sujuan , Tang Bo
Published: June 2020

We propose a stable and ultrasensitive Au–Se SERS nanoprobes for bioimaging and in situ quantitation, which is aim at breaking through the limitations of Au–S SERS nanoprobes, such as interference of biothiols, and unsatisfactory SERS efficiency.
On the impact of metal ion proportion on the physical properties of heterometallic metal–organic frameworks
Authors: Trzmiel Justyna , Peksa Paulina , Ptak Maciej , Fedoruk Katarzyna , Sieradzki Adam
Published: June 2020

In the studied heterometallic structures, the interactions between the built-in EtA+ cation and the environment are modified by the K/Na ratio.
Effect of electron-withdrawing moieties on mechanochromism of phenothiazine derivatives
Authors: Zhang Tong , Han Yanning , Huo Jianzhong , Xue Pengchong
Published: June 2020

Two phenothiazine derivatives with electron-withdrawing cyano and ester groups emitted longer wavelength fluorescence and exhibited different mechanochromic behaviors.
A contrastive study on the properties of plasmon-induced electrons generated from prism- and column-shaped nanoparticles
Authors: Niu Youchen , Sang Lixia
Published: June 2020

Plasmonic metal nanoparticles with anisotropic shapes have different sizes in different directions but influence of this property on plasmon-induced electrons are rarely studied; in particular, a contrastive study among different shapes is lacking.
Salt-induced LCST-type thermal gelation of methylcellulose: quantifying non-specific interactionsviafluctuation theory
Authors: Isobe Noriyuki , Shimizu Seishi
Published: June 2020

Kirkwood–Buff integrals show the accumulation of salts inhibits and the depletion of salts promotes the LCST-type thermal gelation of methylcellulose.
CO adsorption on the calcite(10.4) surface: a combined experimental and theoretical study
Authors: Hafshejani Tahereh Mohammadi , Wang Weijia , Heggemann Jonas , Nefedov Alexei , Heissler Stefan , Wang Yuemin , Rahe Philipp , Thissen Peter , Wöll Christof
Published: June 2020

Information on structural, chemical and physical properties of natural cleaved (10.4) calcite surfaces was obtained by a combined atomic force microscopy and infrared study using CO as a probe molecule under ultrahigh vacuum conditions.
Promoting effects of SO42− on a NiMo/γ-Al2O3 hydrodesulfurization catalyst
Authors: Liu Zhiwei , Han Wei , Hu Dawei , Nie Hong , Wang Zhen , Sun Shuling , Deng Zhonghuo , Yang Qinghe
Published: June 2020

SO42− anchors to a NiMo/γ-Al2O3 catalyst, weakening the metal–support interactions, inhibiting MoS2 aggregation, increasing the number of Ni–Mo–S sites, and thus improving its activity and stability.
CoMoO4/bamboo charcoal hybrid material for high-energy-density and high cycling stability supercapacitors
Authors: Chen Hui , Hu Haiman , Han Fei , Liu Jingdong , Zhang Yurong , Zheng Yuanhui
Published: June 2020

Here we report a supercapacitor with high energy density and high cycling stability using low-cost and environmentally friendly CoMoO4/bamboo charcoal (BC) hybrid materials as the cathode.