bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks
Authors: Clark Natalie M. , Buckner Eli , Fisher Adam P. , Nelson Emily C. , Nguyen Thomas T. , Simmons Abigail R. , de Luis Balaguer Maria A. , Butler-Smith Tiara , Sheldon Parnell J. , Bergmann Dominique C. , Williams Cranos M. , Sozzani Rossangela 
Published: December 2019

AbstractStem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.
CSB promoter downregulation via histone H3 hypoacetylation is an early determinant of replicative senescence
Authors: Crochemore Clément , Fernández-Molina Cristina , Montagne Benjamin , Salles Audrey , Ricchetti Miria 
Published: December 2019

AbstractCellular senescence has causative links with ageing and age-related diseases, however, it remains unclear if progeroid factors cause senescence in normal cells. Here, we show that depletion of CSB, a protein mutated in progeroid Cockayne syndrome (CS), is the earliest known trigger of p21-dependent replicative senescence. CSB depletion promotes overexpression of the HTRA3 protease resulting in mitochondrial impairments, which are causally linked to CS pathological phenotypes. The CSB promoter is downregulated by histone H3 hypoacetylation during DNA damage-response. Mechanistically, CSB binds to the p21 promoter thereby downregulating its transcription and blocking replicative senescence in a p53-independent manner. This activity of CSB is independent of its role in the repair of UV-induced DNA damage. HTRA3 accumulation and senescence are partially rescued upon reduction of oxidative/nitrosative stress. These findings establish a CSB/p21 axis that acts as a barrier to replicative senescence, and link a progeroid factor with the process of regular ageing in human.
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data
Authors: Fang Li , Kao Charlly , Gonzalez Michael V. , Mafra Fernanda A. , Pellegrino da Silva Renata , Li Mingyao , Wenzel Sören-Sebastian , Wimmer Katharina , Hakonarson Hakon , Wang Kai 
Published: December 2019

AbstractLinked-read sequencing provides long-range information on short-read sequencing data by barcoding reads originating from the same DNA molecule, and can improve detection and breakpoint identification for structural variants (SVs). Here we present LinkedSV for SV detection on linked-read sequencing data. LinkedSV considers barcode overlapping and enriched fragment endpoints as signals to detect large SVs, while it leverages read depth, paired-end signals and local assembly to detect small SVs. Benchmarking studies demonstrate that LinkedSV outperforms existing tools, especially on exome data and on somatic SVs with low variant allele frequencies. We demonstrate clinical cases where LinkedSV identifies disease-causal SVs from linked-read exome sequencing data missed by conventional exome sequencing, and show examples where LinkedSV identifies SVs missed by high-coverage long-read sequencing. In summary, LinkedSV can detect SVs missed by conventional short-read and long-read sequencing approaches, and may resolve negative cases from clinical genome/exome sequencing studies.
Quantum engineered Kondo lattices
Authors: Figgins Jeremy , Mattos Laila S. , Mar Warren , Chen Yi-Ting , Manoharan Hari C. , Morr Dirk K. 
Published: December 2019

AbstractAtomic manipulation techniques have provided a bottom-up approach to investigating the unconventional properties and complex phases of strongly correlated electron materials. By engineering artificial systems containing tens to thousands of atoms with tailored electronic or magnetic properties, it has become possible to explore how quantum many-body effects emerge as the size of a system is increased from the nanoscale to the mesoscale. Here we investigate both theoretically and experimentally the quantum engineering of nanoscale Kondo lattices – Kondo droplets – exemplifying nanoscopic replicas of heavy-fermion materials. We demonstrate that by changing a droplet’s real-space geometry, we can not only create coherently coupled Kondo droplets whose properties asymptotically approach those of a quantum-coherent Kondo lattice, but also markedly increase or decrease the droplet’s Kondo temperature. Furthermore we report on the discovery of a new quantum phenomenon – the Kondo echo – a signature of droplets containing Kondo holes functioning as direct probes of spatially extended, quantum-coherent Kondo cloud correlations.
Short-term availability of adult-born neurons for memory encoding
Authors: Forest Jérémy , Moreno Mélissa , Cavelius Matthias , Chalençon Laura , Ziessel Anne , Sacquet Joëlle , Richard Marion , Didier Anne , Mandairon Nathalie 
Published: December 2019

AbstractAdult olfactory neurogenesis provides waves of new neurons involved in memory encoding. However, how the olfactory bulb deals with neuronal renewal to ensure the persistence of pertinent memories and the flexibility to integrate new events remains unanswered. To address this issue, mice performed two successive olfactory discrimination learning tasks with varying times between tasks. We show that with a short time between tasks, adult-born neurons supporting the first learning task appear to be highly sensitive to interference. Furthermore, targeting these neurons using selective light-induced inhibition altered memory of this first task without affecting that of the second, suggesting that neurons in their critical period of integration may only support one memory trace. A longer period between the two tasks allowed for an increased resilience to interference. Hence, newly formed adult-born neurons regulate the transience or persistence of a memory as a function of information relevance and retrograde interference.
High-resolution label-free 3D mapping of extracellular pH of single living cells
Authors: Zhang Yanjun , Takahashi Yasufumi , Hong Sung Pil , Liu Fengjie , Bednarska Joanna , Goff Philip S. , Novak Pavel , Shevchuk Andrew , Gopal Sahana , Barozzi Iros , Magnani Luca , Sakai Hideki , Suguru Yoshimoto , Fujii Takuto , Erofeev Alexander , Gorelkin Peter , Majouga Alexander , Weiss Dominik J. , Edwards Christopher , Ivanov Aleksandar P. , Klenerman David , Sviderskaya Elena V. , Edel Joshua B. , Korchev Yuri 
Published: December 2019

AbstractDynamic mapping of extracellular pH (pHe) at the single-cell level is critical for understanding the role of H+ in cellular and subcellular processes, with particular importance in cancer. While several pHe sensing techniques have been developed, accessing this information at the single-cell level requires improvement in sensitivity, spatial and temporal resolution. We report on a zwitterionic label-free pH nanoprobe that addresses these long-standing challenges. The probe has a sensitivity > 0.01 units, 2 ms response time, and 50 nm spatial resolution. The platform was integrated into a double-barrel nanoprobe combining pH sensing with feedback-controlled distance dependance via Scanning Ion Conductance Microscopy. This allows for the simultaneous 3D topographical imaging and pHe monitoring of living cancer cells. These classes of nanoprobes were used for real-time high spatiotemporal resolution pHe mapping at the subcellular level and revealed tumour heterogeneity of the peri-cellular environments of melanoma and breast cancer cells.
Programmable and robust static topological solitons in mechanical metamaterials
Authors: Zhang Yafei , Li Bo , Zheng Q. S. , Genin Guy M. , Chen C. Q. 
Published: December 2019

AbstractSolitary, persistent wave packets called solitons hold potential to transfer information and energy across a wide range of spatial and temporal scales in physical, chemical, and biological systems. Mechanical solitons characteristically emerge either as a single wave packet or uncorrelated propagating topological entities through space and/or time, but these are notoriously difficult to control. Here, we report a theoretical framework for programming static periodic topological solitons into a metamaterial, and demonstrate its implementation in real metamaterials computationally and experimentally. The solitons are excited by deformation localizations under quasi-static compression, and arise from buckling-induced kink-antikink bands that provide domain separation barriers. The soliton number and wavelength demonstrate a previously unreported size-dependence, due to intrinsic length scales. We identify that these unanticipated solitons stem from displacive phase transitions with periodic topological excitations captured by the well-known $${\varphi }^{4}$$

φ

4

theory. Results reveal pathways for robust regularizations of stochastic responses of metamaterials.
NAIL-MS reveals the repair of 2-methylthiocytidine by AlkB in E. coli
Authors: Reichle Valentin F. , Petrov Dimitar P. , Weber Verena , Jung Kirsten , Kellner Stefanie 
Published: December 2019

AbstractRNAs contain post-transcriptional modifications, which fulfill a variety of functions in translation, secondary structure stabilization and cellular stress survival. Here, 2-methylthiocytidine (ms2C) is identified in tRNA of E. coli and P. aeruginosa using NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) in combination with genetic screening experiments. ms2C is only found in 2-thiocytidine (s2C) containing tRNAs, namely tRNAArgCCG, tRNAArgICG, tRNAArgUCU and tRNASerGCU at low abundances. ms2C is not formed by commonly known tRNA methyltransferases. Instead, we observe its formation in vitro and in vivo during exposure to methylating agents. More than half of the s2C containing tRNA can be methylated to carry ms2C. With a pulse-chase NAIL-MS experiment, the repair mechanism by AlkB dependent sulfur demethylation is demonstrated in vivo. Overall, we describe ms2C as a bacterial tRNA modification and damage product. Its repair by AlkB and other pathways is demonstrated in vivo by our powerful NAIL-MS approach.
Chromosome-associated RNA–protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe
Authors: Ding Da-Qiao , Okamasa Kasumi , Katou Yuki , Oya Eriko , Nakayama Jun-ichi , Chikashige Yuji , Shirahige Katsuhiko , Haraguchi Tokuko , Hiraoka Yasushi 
Published: December 2019

AbstractPairing of homologous chromosomes in meiosis is essential for sexual reproduction. We have previously demonstrated that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 chromosomal loci and mediates their robust pairing in meiosis. However, the mechanisms underlying lncRNA-mediated homologous pairing have remained elusive. In this study, we identify conserved RNA-binding proteins that are required for robust pairing of homologous chromosomes. These proteins accumulate mainly at the sme2 and two other chromosomal loci together with meiosis-specific lncRNAs transcribed from these loci. Remarkably, the chromosomal accumulation of these lncRNA–protein complexes is required for robust pairing. Moreover, the lncRNA–protein complexes exhibit phase separation properties, since 1,6-hexanediol treatment reversibly disassembled these complexes and disrupted the pairing of associated loci. We propose that lncRNA–protein complexes assembled at specific chromosomal loci mediate recognition and subsequent pairing of homologous chromosomes.
Optimal verification of general bipartite pure states
Authors: Yu Xiao-Dong , Shang Jiangwei , Gühne Otfried 
Published: December 2019

AbstractThe efficient and reliable verification of quantum states plays a crucial role in various quantum information processing tasks. We consider the task of verifying entangled states using one-way and two-way classical communication and completely characterize the optimal strategies via convex optimization. We solve these optimization problems using both analytical and numerical methods, and the optimal strategies can be constructed for any bipartite pure state. Compared with the nonadaptive approach, our adaptive strategies significantly improve the efficiency of quantum state verification. Moreover, these strategies are experimentally feasible, as only few local projective measurements are required.
Mitigation of acyl-homoserine lactone (AHL) based bacterial quorum sensing, virulence functions, and biofilm formation by yttrium oxide core/shell nanospheres: Novel approach to combat drug resistance
Authors: Husain Fohad Mabood , Ansari Anees A. , Khan Aslam , Ahmad Naushad , Albadri Abdulrahman , Albalawi Thamer H. 
Published: December 2019

AbstractThe present study evaluated the efficacy of Y2O3:Tb (core) and Y2O3:Tb@SiO2 nanospheres (core/shell NSs) against virulence functions regulated by quorum sensing (QS) and biofilm formation in pathogenic bacteria. Scanning electron microscope (SEM) images were used to study the size, shape, and morphology. The images clearly displayed spherical shaped, mono-dispersed particles with narrow size distribution and an average grain size of 110–130 nm. The chemical composition of the samples was determined by using energy dispersive X-ray (EDX) and X-ray photoelectron spectroscopy (XPS). We determined the impact of core and core/shell NSs on QS using sensor strains of Chromobacterium violaceum CVO26 and Pseudomonas aeruginosa PAO1 in a comparative study. Sub-MICs of core and core/shell NSs substantially suppressed QS-controlled violacein production in C. violaceum. Similar concentration-dependent effect of sub-MICs of synthesized core and core/shell NSs was observed in the QS-regulated virulence functions (elastase, total protease, pyocyanin production, swarming motility, and exopolysaccharide production) in PAO1. A concentration-dependent decrease (14–60%) was recorded in the biofilm forming capability of PAO1, upon treatment with core and core/shell NSs. Moreover, core/shell NSs were more effective in inhibiting biofilm at higher tested concentrations as compared to core-NSs. The synthesized NSs demonstrated significantly impaired attachment of cells to the microtiter plate indicating that NSs target biofilm inhibition at the attachment stage. Based on these results, we predict that core and core/shell NSs may be an alternative to combat the threat of drug-resistant pathogenic bacteria.
Two-dimensional Tunable Dirac/Weyl Semimetal in Non-Abelian Gauge Field
Authors: Guo Yaowu , Lin Zhi , Zhao Jia-Qiang , Lou Jie , Chen Yan 
Published: December 2019

AbstractThree-dimensional(3D) Weyl semimetal(WSM) with linear energy spectra has attracted significant interest. Especially they have been observed experimentally in several solid materials with the breaking of inversion symmetry. Here we predict a new family of particle-hole($${\mathscr{C}}$$
C
) invariant 2D WSMs in the non-Abelian gauge field, which can emerge in the low energy bands being close to Fermi energy (dubbed Weyl-I) and the high energy bands being away from Fermi energy (dubbed Weyl-II), only when the time-reversal symmetry($${\mathscr{T}}$$
T
) of the 2D Dirac semimetal is broken in the presence of in-plane Zeeman fields. Moreover, a 2D Dirac node can split into a pair of Weyl nodes showing the same Berry phase, and the 2D WSM, being protected by $${\mathscr{T}}$$
T
symmetry, exhibits four Weyl-I nodes, whose energies are invariant with the variation of the magnetic field. The corresponding Fermi velocity and Berry connection have been calculated. Based on the 2D WSMs, we also examine inhomogeneous pairings of attractive Fermi gases and find a new kind of the LO states with the beat frequency. This 2D WSM provides a realistic and promising platform for exploring and manipulating exotic Weyl physics, which may increase the experimental feasibility in the context of ultracold atoms.
Molecular Characterization of Methicillin- Resistant Staphylococcus aureus in a Tertiary Care hospital in Kuwait
Authors: Alfouzan Wadha , Udo Edet E. , Modhaffer Azizah , Alosaimi Asma’a 
Published: December 2019

AbstractMethicillin-resistant Staphylococcus aureus (MRSA) are a major cause of healthcare and community- associated infections due to their ability to express a variety of virulence factors. We investigated 209 MRSA isolates obtained from 1 January to 31 December 2016 using a combination of phenotypic and genotypic methods to understand the genetic backgrounds of MRSA strains obtained in a General hospital in Kuwait. Antibiotics susceptibility was performed with disk diffusion, and MIC was measured with Etest strips. Molecular typing was performed using SCCmec typing, spa typing, and DNA microarray for antibiotic resistance and virulence genes. The isolates were susceptible to vancomycin, teicoplanin, rifampicin, ceftaroline, and linezolid but were resistant to gentamicin, tetracycline, erythromycin, fusidic acid, chloramphenicol and ciprofloxacin. Molecular typing revealed six SCCmec types, 56 spa types and 16 clonal complexes (CC). The common SCCmec types were type IV (39.5%), type III (34.4%), type V (25.8%) and type VI (3.8%). The dominant spa types were t860 (23.9%), t945 (8.6%), t127 (6.7%), t688 (6.7%), t304 (6.2) and t044 (5.7%). The other spa types occurred sporadically. Genes for PVL was detected in 59 (28.2%) of the isolates. CC8-ST239-MRSA-III + SCCmer (23.3%) was the most prevalent clone, followed by CC6-MRSA-IV (8.3%), CC80-MRSA-IV [PVL+] (5.8%), CC5-MRSA-VI + SCCfus (5.0%), CC30-MRSA-IV[PVL+] (4.1%), CC1-MRSA-V + SCCfus [PVL+] (4.1%), CC5-MRSA-V + SCCfus (4.1%) and CC22-MRSA-IV[PVL+] (4.1%). The study revealed that despite the emergence of MRSA with diverse genetic backgrounds over the years, ST239-MRSA-III remained the dominant clone in the hospital. This warrants reassessment of infection prevention and control procedures at this hospital.
The expression pattern of OsDim1 in rice and its proposed function
Authors: Doku Henry Akrofi , Gan Shu-Xian , Zhu Qian , Nadir Sadia , Li Wei , Li Meng-Ting , Zhou Li , Li Cheng-Yun , Kang Sang-Gu , Park Eui-Ho , Chen Li-Juan , Lee Dong-Sun 
Published: December 2019

AbstractDevelopment of plant tissues is dependent on numerous factors, including hormone activity, signaling, cell division, and elongation. In plants, Defective Entry into Mitosis 1 (Dim1) homologs are recognized as pivotal in leaf senescence and progress of normal growth, but their role in rice has not been functionally characterized. The findings presented in this paper suggest that OsDim1 is important in early seedling development, pollen tube elongation, and impacts rice yield components. The gene is expressed in the scutellum, endosperm, embryonic root, shoot, pollen grains and tubes, as well as in several organs of the rice flower. According to the present study findings, RNAi mediated knockdown of OsDim1 resulted in phytohormonal imbalance, reduced amylase activity, affected differentiation of embryonic root elongation zone tissues, suppressed embryonic root and shoot growth, and impaired pollen tube elongation. In contrast, overexpression of OsDim1 showed significant growth in embryonic roots and shoots, while it increased culm length, total number of tillers per plant, seed setting rate, and total number of grains per panicle compared to its wild type line. In summary, we propose OsDim1 plays an important role in seedling growth and pollen tube elongation, and has pleiotropic effects on reproductive tissues.
Unravelling Receptor and RGD Motif Dependence of Retargeted Adenoviral Vectors using Advanced Tumor Model Systems
Authors: Chernyavska M. , Schmid M. , Freitag P. C. , Palacio-Castañeda V. , Piruska A. , Huck W. T. S. , Plückthun A. , Verdurmen W. P. R. 
Published: December 2019

AbstractRecent advances in engineering adenoviruses are paving the way for new therapeutic gene delivery approaches in cancer. However, there is limited knowledge regarding the impact of adenoviral retargeting on transduction efficiency in more complex tumor architectures, and the role of the RGD loop at the penton base in retargeting is unclear. To address this gap, we used tumor models of increasing complexity to study the role of the receptor and the RGD motif. Employing tumor-fibroblast co-culture models, we demonstrate the importance of the RGD motif for efficient transduction in 2D through the epithelial cell adhesion molecule (EpCAM), but not the epidermal growth factor receptor (EGFR). Via optical clearing of co-culture spheroids, we show that the RGD motif is required for transduction via both receptors in 3D tumor architectures. We subsequently employed a custom-designed microfluidic model containing collagen-embedded tumor spheroids, mimicking the interplay between interstitial flow, extracellular matrix and adenoviral transduction. Image analysis of on-chip cleared spheroids indicated the importance of the RGD motif for on-chip adenoviral transduction. Together, our results show the interrelationship between receptor characteristics, the RGD motif, the 3D tumor architecture and retargeted adenoviral transduction efficiency. The findings are important for the rational design of next-generation therapeutic adenoviruses.
Quantitative trait loci influencing pentacyclic triterpene composition in apple fruit peel
Authors: Christeller John T. , McGhie Tony K. , Johnston Jason W. , Carr Bridie , Chagné David 
Published: December 2019

AbstractThe chemical composition of pentacyclic triterpenes was analysed using a ‘Royal Gala’ x ‘Granny Smith’ segregating population in 2013 and 2015, using apple peels extracted from mature fruit at harvest and after 12 weeks of cold storage. In 2013, 20 compound isoforms from nine unique compound classes were measured for both treatments. In 2015, 20 and 17 compound isoforms from eight unique compound classes were measured at harvest and after cold storage, respectively. In total, 68 quantitative trait loci (QTLs) were detected on 13 linkage groups (LG). Thirty two and 36 QTLs were detected for compounds measured at harvest and after cold storage, respectively. The apple chromosomes with the most QTLs were LG3, LG5, LG9 and LG17. The largest effect QTL was for trihydroxy-urs-12-ene-28-oic acid, located on LG5; this was measured in 2015 after storage, and was inherited from the ‘Royal Gala’ parent (24.9% of the phenotypic variation explained).