bluuebunny/crossref_metadata_2025_split huggingface dataset:
METTL3 regulates WTAP protein homeostasis
Authors: Sorci Melissa , Ianniello Zaira , Cruciani Sonia , Larivera Simone , Ginistrelli Lavinia Ceci , Capuano Ernestina , Marchioni Marcella , Fazi Francesco , Fatica Alessandro 
Published: July 2018

AbstractThe Wilms tumor 1 (WT1)-associated protein (WTAP) is upregulated in many tumors, including, acute myeloid leukemia (AML), where it plays an oncogenic role by interacting with different proteins involved in RNA processing and cell proliferation. In addition, WTAP is also a regulator of the nuclear complex required for the deposition of N6-methyladenosine (m6A) into mRNAs, containing the METTL3 methyltransferase. However, it is not clear if WTAP may have m6A-independent regulatory functions that might contribute to its oncogenic role. Here, we show that both knockdown and overexpression of METTL3 protein results in WTAP protein upregulation, indicating that METTL3 levels are critical for WTAP protein homeostasis. However, we show that WTAP upregulation is not sufficient to promote cell proliferation in the absence of a functional METTL3. Therein, these data indicate that the reported oncogenic function of WTAP is strictly connected to a functional m6A methylation complex.
Mitochondrial dynamics regulates Drosophila intestinal stem cell differentiation
Authors: Deng Hansong , Takashima Shigeo , Paul Manash , Guo Ming , Hartenstein Volker 
Published: July 2018

AbstractDifferentiation of stem/progenitor cells is associated with a substantial increase in mitochondrial mass and complexity. Mitochondrial dynamics, including the processes of fusion and fission, plays an important role for somatic cell reprogramming and pluripotency maintenance in induced pluripotent cells (iPSCs). However, the role of mitochondrial dynamics during stem/progenitor cell differentiation in vivo remains elusive. Here we found differentiation of Drosophila intestinal stem cell is accompanied with continuous mitochondrial fusion. Mitochondrial fusion defective(opa1RNAi) ISCs contain less mitochondrial membrane potential, reduced ATP, and increased ROS level. Surprisingly, suppressing fusion also resulted in the failure of progenitor cells to differentiate. Cells did not switch on the expression of differentiation markers, and instead continued to show characteristics of progenitor cells. Meanwhile, proliferation or apoptosis was unaffected. The differentiation defect could be rescued by concomitant inhibition of Drp1, a mitochondrial fission molecule. Moreover, ROS scavenger also partially rescues opa1RNAi-associated differentiation defects via down-regulating JNK activity. We propose that mitochondrial fusion plays a pivotal role in controlling the developmental switch of stem cell fate.
Chemically specific termination control of oxide interfaces via layer-by-layer mean inner potential engineering
Authors: Sun H. Y. , Mao Z. W. , Zhang T. W. , Han L. , Zhang T. T. , Cai X. B. , Guo X. , Li Y. F. , Zang Y. P. , Guo W. , Song J. H. , Ji D. X. , Gu C. Y. , Tang C. , Gu Z. B. , Wang N. , Zhu Y. , Schlom D. G. , Nie Y. F. , Pan X. Q. 
Published: July 2018

AbstractCreating oxide interfaces with precise chemical specificity at the atomic layer level is desired for the engineering of quantum phases and electronic applications, but highly challenging, owing partially to the lack of in situ tools to monitor the chemical composition and completeness of the surface layer during growth. Here we report the in situ observation of atomic layer-by-layer inner potential variations by analysing the Kikuchi lines during epitaxial growth of strontium titanate, providing a powerful real-time technique to monitor and control the chemical composition during growth. A model combining the effects of mean inner potential and step edge density (roughness) reveals the underlying mechanism of the complex and previously not well-understood reflection high-energy electron diffraction oscillations observed in the shuttered growth of oxide films. General rules are proposed to guide the synthesis of atomically and chemically sharp oxide interfaces, opening up vast opportunities for the exploration of intriguing quantum phenomena at oxide interfaces.
Persistent CO2 emissions and hydrothermal unrest following the 2015 earthquake in Nepal
Authors: Girault Frédéric , Adhikari Lok Bijaya , France-Lanord Christian , Agrinier Pierre , Koirala Bharat P. , Bhattarai Mukunda , Mahat Sudhan S. , Groppo Chiara , Rolfo Franco , Bollinger Laurent , Perrier Frédéric 
Published: July 2018

AbstractFluid–earthquake interplay, as evidenced by aftershock distributions or earthquake-induced effects on near-surface aquifers, has suggested that earthquakes dynamically affect permeability of the Earth’s crust. The connection between the mid-crust and the surface was further supported by instances of carbon dioxide (CO2) emissions associated with seismic activity, so far only observed in magmatic context. Here we report spectacular non-volcanic CO2 emissions and hydrothermal disturbances at the front of the Nepal Himalayas following the deadly 25 April 2015 Gorkha earthquake (moment magnitude Mw = 7.8). The data show unambiguously the appearance, after the earthquake, sometimes with a delay of several months, of CO2 emissions at several sites separated by > 10 kilometres, associated with persistent changes in hydrothermal discharges, including a complete cessation. These observations reveal that Himalayan hydrothermal systems are sensitive to co- and post- seismic deformation, leading to non-stationary release of metamorphic CO2 from active orogens. Possible pre-seismic effects need further confirmation.
A framework for enhancing ethical genomic research with Indigenous communities
Authors: Claw Katrina G. , Anderson Matthew Z. , Begay Rene L. , Tsosie Krystal S. , Fox Keolu , Garrison Nanibaa’ A. ,   Summer internship for INdigenous peoples in Genomics (SING) Consortium, Bader Alyssa C. , Bardill Jessica , Bolnick Deborah A. , Brooks Jada , Cordova Anna , Malhi Ripan S. , Nakatsuka Nathan , Neller Angela , Raff Jennifer A. , Singson Jamie , TallBear Kim , Vargas Tada , Yracheta Joseph M. 
Published: July 2018

AbstractIntegration of genomic technology into healthcare settings establishes new capabilities to predict disease susceptibility and optimize treatment regimes. Yet, Indigenous peoples remain starkly underrepresented in genetic and clinical health research and are unlikely to benefit from such efforts. To foster collaboration with Indigenous communities, we propose six principles for ethical engagement in genomic research: understand existing regulations, foster collaboration, build cultural competency, improve research transparency, support capacity building, and disseminate research findings. Inclusion of underrepresented communities in genomic research has the potential to expand our understanding of genomic influences on health and improve clinical approaches for all populations.
The influence of Arctic amplification on mid-latitude summer circulation
Authors: Coumou D. , Di Capua G. , Vavrus S. , Wang L. , Wang S. 
Published: July 2018

AbstractAccelerated warming in the Arctic, as compared to the rest of the globe, might have profound impacts on mid-latitude weather. Most studies analyzing Arctic links to mid-latitude weather focused on winter, yet recent summers have seen strong reductions in sea-ice extent and snow cover, a weakened equator-to-pole thermal gradient and associated weakening of the mid-latitude circulation. We review the scientific evidence behind three leading hypotheses on the influence of Arctic changes on mid-latitude summer weather: Weakened storm tracks, shifted jet streams, and amplified quasi-stationary waves. We show that interactions between Arctic teleconnections and other remote and regional feedback processes could lead to more persistent hot-dry extremes in the mid-latitudes. The exact nature of these non-linear interactions is not well quantified but they provide potential high-impact risks for society.
Exploiting a cognitive bias promotes cooperation in social dilemma experiments
Authors: Wang Zhen , Jusup Marko , Shi Lei , Lee Joung-Hun , Iwasa Yoh , Boccaletti Stefano 
Published: July 2018

AbstractThe decoy effect is a cognitive bias documented in behavioural economics by which the presence of a third, (partly) inferior choice causes a significant shift in people’s preference for other items. Here, we performed an experiment with human volunteers who played a variant of the repeated prisoner’s dilemma game in which the standard options of “cooperate” and “defect” are supplemented with a new, decoy option, “reward”. We show that although volunteers rarely chose the decoy option, its availability sparks a significant increase in overall cooperativeness and improves the likelihood of success for cooperative individuals in this game. The presence of the decoy increased willingness of volunteers to cooperate in the first step of each game, leading to subsequent propagation of such willingness by (noisy) tit-for-tat. Our study thus points to decoys as a means to elicit voluntary prosocial action across a spectrum of collective endeavours.
Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes
Authors: Janečka Jan E. , Davis Brian W. , Ghosh Sharmila , Paria Nandina , Das Pranab J. , Orlando Ludovic , Schubert Mikkel , Nielsen Martin K. , Stout Tom A. E. , Brashear Wesley , Li Gang , Johnson Charles D. , Metz Richard P. , Zadjali Al Muatasim Al , Love Charles C. , Varner Dickson D. , Bellott Daniel W. , Murphy William J. , Chowdhary Bhanu P. , Raudsepp Terje 
Published: July 2018

AbstractDynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X–Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.
A facile strategy for realizing room temperature phosphorescence and single molecule white light emission
Authors: Wang Jianguo , Gu Xinggui , Ma Huili , Peng Qian , Huang Xiaobo , Zheng Xiaoyan , Sung Simon H. P. , Shan Guogang , Lam Jacky W. Y. , Shuai Zhigang , Tang Ben Zhong 
Published: July 2018

AbstractResearch on materials with pure organic room temperature phosphorescence (RTP) and their application as organic single-molecule white light emitters is a hot area and relies on the design of highly efficient pure organic RTP luminogens. Herein, a facile strategy of heavy-atom-participated anion–π+ interactions is proposed to construct RTP-active organic salt compounds (1,2,3,4-tetraphenyloxazoliums with different counterions). Those compounds with heavy-atom counterions (bromide and iodide ions) exhibit outstanding RTP due to the external heavy atom effect via anion–π+ interactions, evidently supported by the single-crystal X-ray diffraction analysis and theoretical calculation. Their single-molecule white light emission is realized by tuning the degree of crystallization. Such white light emission also performs well in polymer matrices and their use in 3D printing is demonstrated by white light lampshades.
Designing with living systems in the synthetic yeast project
Authors: Szymanski Erika , Calvert Jane 
Published: July 2018

AbstractSynthetic biology is challenged by the complexity and the unpredictability of living systems. While one response to this complexity involves simplifying cells to create more fully specified systems, another approach utilizes directed evolution, releasing some control and using unpredictable change to achieve design goals. Here we discuss SCRaMbLE, employed in the synthetic yeast project, as an example of synthetic biology design through working with living systems. SCRaMbLE is a designed tool without being a design tool, harnessing the activities of the yeast rather than relying entirely on scientists’ deliberate choices. We suggest that directed evolution at the level of the whole organism allows scientists and microorganisms to “collaborate” to achieve design goals, suggesting new directions for synthetic biology.
Spindle tubulin and MTOC asymmetries may explain meiotic drive in oocytes
Authors: Wu Tianyu , Lane Simon I. R. , Morgan Stephanie L. , Jones Keith T. 
Published: July 2018

AbstractIn the first meiotic division (MI) of oocytes, the cortically positioned spindle causes bivalent segregation in which only the centre-facing homologue pairs are retained. ‘Selfish’ chromosomes are known to exist, which bias their spindle orientation and hence retention in the egg, a process known as ‘meiotic drive’. Here we report on this phenomenon in oocytes from F1 hybrid mice, where parental strain differences in centromere size allows distinction of the two homologue pairs of a bivalent. Bivalents with centromere and kinetochore asymmetry show meiotic drive by rotating during prometaphase, in a process dependent on aurora kinase activity. Cortically positioned homologue pairs appear to be under greater stretch than their centre-facing partners. Additionally the cortex spindle-half contain a greater density of tubulin and microtubule organising centres. A model is presented in which meiotic drive is explained by the impact of microtubule force asymmetry on chromosomes with different sized centromeres and kinetochores.
Macrophages are exploited from an innate wound healing response to facilitate cancer metastasis
Authors: Muliaditan Tamara , Caron Jonathan , Okesola Mary , Opzoomer James W. , Kosti Paris , Georgouli Mirella , Gordon Peter , Lall Sharanpreet , Kuzeva Desislava M. , Pedro Luisa , Shields Jacqueline D. , Gillett Cheryl E. , Diebold Sandra S. , Sanz-Moreno Victoria , Ng Tony , Hoste Esther , Arnold James N. 
Published: July 2018

AbstractTumour-associated macrophages (TAMs) play an important role in tumour progression, which is facilitated by their ability to respond to environmental cues. Here we report, using murine models of breast cancer, that TAMs expressing fibroblast activation protein alpha (FAP) and haem oxygenase-1 (HO-1), which are also found in human breast cancer, represent a macrophage phenotype similar to that observed during the wound healing response. Importantly, the expression of a wound-like cytokine response within the tumour is clinically associated with poor prognosis in a variety of cancers. We show that co-expression of FAP and HO-1 in macrophages results from an innate early regenerative response driven by IL-6, which both directly regulates HO-1 expression and licenses FAP expression in a skin-like collagen-rich environment. We show that tumours can exploit this response to facilitate transendothelial migration and metastatic spread of the disease, which can be pharmacologically targeted using a clinically relevant HO-1 inhibitor.
Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects
Authors: Ubels Joske , Sonneveld Pieter , van Beers Erik H. , Broijl Annemiek , van Vliet Martin H. , de Ridder Jeroen 
Published: July 2018

AbstractMany cancer treatments are associated with serious side effects, while they often only benefit a subset of the patients. Therefore, there is an urgent clinical need for tools that can aid in selecting the right treatment at diagnosis. Here we introduce simulated treatment learning (STL), which enables prediction of a patient’s treatment benefit. STL uses the idea that patients who received different treatments, but have similar genetic tumor profiles, can be used to model their response to the alternative treatment. We apply STL to two multiple myeloma gene expression datasets, containing different treatments (bortezomib and lenalidomide). We find that STL can predict treatment benefit for both; a twofold progression free survival (PFS) benefit is observed for bortezomib for 19.8% and a threefold PFS benefit for lenalidomide for 31.1% of the patients. This demonstrates that STL can derive clinically actionable gene expression signatures that enable a more personalized approach to treatment.
Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution
Authors: Zhou Qin , Kaappa Sami , Malola Sami , Lu Hui , Guan Dawei , Li Yajuan , Wang Haochen , Xie Zhaoxiong , Ma Zhibo , Häkkinen Hannu , Zheng Nanfeng , Yang Xueming , Zheng Lansun 
Published: July 2018

AbstractHigh-resolution real-space imaging of nanoparticle surfaces is desirable for better understanding of surface composition and morphology, molecular interactions at the surface, and nanoparticle chemical functionality in its environment. However, achieving molecular or sub-molecular resolution has proven to be very challenging, due to highly curved nanoparticle surfaces and often insufficient knowledge of the monolayer composition. Here, we demonstrate sub-molecular resolution in scanning tunneling microscopy imaging of thiol monolayer of a 5 nm nanoparticle Ag374 protected by tert-butyl benzene thiol. The experimental data is confirmed by comparisons through a pattern recognition algorithm to simulated topography images from density functional theory using the known total structure of the Ag374 nanocluster. Our work demonstrates a working methodology for investigations of structure and composition of organic monolayers on curved nanoparticle surfaces, which helps designing functionalities for nanoparticle-based applications.
Scutoids are a geometrical solution to three-dimensional packing of epithelia
Authors: Gómez-Gálvez Pedro , Vicente-Munuera Pablo , Tagua Antonio , Forja Cristina , Castro Ana M. , Letrán Marta , Valencia-Expósito Andrea , Grima Clara , Bermúdez-Gallardo Marina , Serrano-Pérez-Higueras Óscar , Cavodeassi Florencia , Sotillos Sol , Martín-Bermudo María D. , Márquez Alberto , Buceta Javier , Escudero Luis M. 
Published: July 2018

AbstractAs animals develop, tissue bending contributes to shape the organs into complex three-dimensional structures. However, the architecture and packing of curved epithelia remains largely unknown. Here we show by means of mathematical modelling that cells in bent epithelia can undergo intercalations along the apico-basal axis. This phenomenon forces cells to have different neighbours in their basal and apical surfaces. As a consequence, epithelial cells adopt a novel shape that we term “scutoid”. The detailed analysis of diverse tissues confirms that generation of apico-basal intercalations between cells is a common feature during morphogenesis. Using biophysical arguments, we propose that scutoids make possible the minimization of the tissue energy and stabilize three-dimensional packing. Hence, we conclude that scutoids are one of nature's solutions to achieve epithelial bending. Our findings pave the way to understand the three-dimensional organization of epithelial organs.
Contact inhibition controls cell survival and proliferation via YAP/TAZ-autophagy axis
Authors: Pavel Mariana , Renna Maurizio , Park So Jung , Menzies Fiona M. , Ricketts Thomas , Füllgrabe Jens , Ashkenazi Avraham , Frake Rebecca A. , Lombarte Alejandro Carnicer , Bento Carla F. , Franze Kristian , Rubinsztein David C. 
Published: July 2018

AbstractContact inhibition enables noncancerous cells to cease proliferation and growth when they contact each other. This characteristic is lost when cells undergo malignant transformation, leading to uncontrolled proliferation and solid tumor formation. Here we report that autophagy is compromised in contact-inhibited cells in 2D or 3D-soft extracellular matrix cultures. In such cells, YAP/TAZ fail to co-transcriptionally regulate the expression of myosin-II genes, resulting in the loss of F-actin stress fibers, which impairs autophagosome formation. The decreased proliferation resulting from contact inhibition is partly autophagy-dependent, as is their increased sensitivity to hypoxia and glucose starvation. These findings define how mechanically repressed YAP/TAZ activity impacts autophagy to contribute to core phenotypes resulting from high cell confluence that are lost in various cancers.
Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells
Authors: Tycko Josh , Barrera Luis A. , Huston Nicholas C. , Friedland Ari E. , Wu Xuebing , Gootenberg Jonathan S. , Abudayyeh Omar O. , Myer Vic E. , Wilson Christopher J. , Hsu Patrick D. 
Published: July 2018

AbstractTherapeutic genome editing with Staphylococcus aureus Cas9 (SaCas9) requires a rigorous understanding of its potential off-target activity in the human genome. Here we report a high-throughput screening approach to measure SaCas9 genome editing variation in human cells across a large repertoire of 88,692 single guide RNAs (sgRNAs) paired with matched or mismatched target sites in a synthetic cassette. We incorporate randomized barcodes that enable whitelisting of correctly synthesized molecules for further downstream analysis, in order to circumvent the limitation of oligonucleotide synthesis errors. We find SaCas9 sgRNAs with 21-mer or 22-mer spacer sequences are generally more active, although high efficiency 20-mer spacers are markedly less tolerant of mismatches. Using this dataset, we developed an SaCas9 specificity model that performs robustly in ranking off-target sites. The barcoded pairwise library screen enabled high-fidelity recovery of guide-target relationships, providing a scalable framework for the investigation of CRISPR enzyme properties and general nucleic acid interactions.
Lighting up silicon nanoparticles with Mie resonances
Authors: Zhang Chengyun , Xu Yi , Liu Jin , Li Juntao , Xiang Jin , Li Hui , Li Jinxiang , Dai Qiaofeng , Lan Sheng , Miroshnichenko Andrey E. 
Published: July 2018

AbstractAs one of the most important semiconductors, silicon has been used to fabricate electronic devices, waveguides, detectors, solar cells, etc. However, the indirect bandgap and low quantum efficiency (10−7) hinder the use of silicon for making good emitters. For integrated photonic circuits, silicon-based emitters with sizes in the range of 100−300 nm are highly desirable. Here, we show the use of the electric and magnetic resonances in silicon nanoparticles to enhance the quantum efficiency and demonstrate the white-light emission from silicon nanoparticles with feature sizes of ~200 nm. The magnetic and electric dipole resonances are employed to dramatically increase the relaxation time of hot carriers, while the magnetic and electric quadrupole resonances are utilized to reduce the radiative recombination lifetime of hot carriers. This strategy leads to an enhancement in the quantum efficiency of silicon nanoparticles by nearly five orders of magnitude as compared with bulk silicon, taking the three-photon-induced absorption into account.