bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractOptical 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

AbstracttRNA-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

Abstract
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

AbstractIdiopathic 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

AbstractThe 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

AbstractStarch 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

AbstractFlavonoids, 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

AbstractFruit 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

AbstractCultivated 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.
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

AbstractAn 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

AbstractHIV-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

AbstractBile 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

AbstractRecently, 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

AbstractWithin 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.