bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo and cell line models of human mammary cell transformation reveal an essential role for Yb-1 in multiple stages of human breast cancer
Authors: Lefort Sylvain , El-Naggar Amal , Tan Susanna , Colborne Shane , Negri Gian Luca , Pellacani Davide , Hirst Martin , Gusterson Barry , Morin Gregg B. , Sorensen Poul H. , Eaves Connie J. 
Published: July 2021

AbstractBreast cancer heterogeneity has made it challenging to identify mechanisms critical to the initial stages of their genesis in vivo. Here, we sought to interrogate the role of YB-1 in newly arising human breast cancers as well as in established cell lines. In a first series of experiments, we found that short-hairpin RNA-mediated knockdown of YB-1 in MDA-MB-231 cells blocked both their local tumour-forming and lung-colonising activity in immunodeficient mice. Conversely, upregulated expression of YB-1 enhanced the poor in vivo tumorigenicity of T47D cells. We then found that YB-1 knockdown also inhibits the initial generation in mice of invasive ductal carcinomas and ductal carcinomas in situ from freshly isolated human mammary cells transduced, respectively, with KRASG12D or myristoylated-AKT1. Interestingly, increased expression of HIF1α and G3BP1, two YB-1 translational targets and elements of a stress-adaptive programme, mirrored the levels of YB-1 in both transformed primary and established MDA-MB-231 breast cancer cells.
PSMC2/CCND1 axis promotes development of ovarian cancer through regulating cell growth, apoptosis and migration
Authors: Zhu Dawei , Huang Jie , Liu Ning , Li Wei , Yan Limei 
Published: July 2021

AbstractOvarian cancer is known as one of the most common malignancies of the gynecological system, whose treatment is still not satisfactory because of the unclear understanding of molecular mechanism. PSMC2 is an essential component of 19 S regulatory granules in 26 S proteasome and its relationship with ovarian cancer is still not clear. In this study, we found that PSMC2 was upregulated in ovarian cancer tissues, associated with tumor grade and could probably predict poor prognosis. Knocking down the endogenous PSMC2 expression in ovarian cancer cells could decrease colony formation ability, cell motility and cell proliferation rate, along with increasing cell apoptosis rate. Cells models or xenografts formed by cells with relatively lower expression of PSMC2 exhibited weaker oncogenicity and slower growth rate in vivo. Moreover, gene microarray was used to analyze the alteration of gene expression profiling of ovarian cancer induced by PSMC2 knockdown and identify CCND1 as a potential downstream of PSMC2. Further study revealed the mutual regulation between PSMC2 and CCND1, and demonstrated that knockdown of CCND1 could enhance the regulatory effects induced by PSMC2 knockdown and overexpression of CCND1 reverses it. In summary, PSMC2 may promote the development of ovarian cancer through CCND1, which may predict poor prognosis of ovarian cancer patients.
Heterotopic ossification in mice overexpressing Bmp2 in Tie2+ lineages
Authors: Prados Belén , del Toro Raquel , MacGrogan Donal , Gómez-Apiñániz Paula , Papoutsi Tania , Muñoz-Cánoves Pura , Méndez-Ferrer Simón , de la Pompa José Luis 
Published: July 2021

AbstractBone morphogenetic protein (Bmp) signaling is critical for organismal development and homeostasis. To elucidate Bmp2 function in the vascular/hematopoietic lineages we generated a new transgenic mouse line in which ectopic Bmp2 expression is controlled by the Tie2 promoter. Tie2CRE/+;Bmp2tg/tg mice develop aortic valve dysfunction postnatally, accompanied by pre-calcific lesion formation in valve leaflets. Remarkably, Tie2CRE/+;Bmp2tg/tg mice develop extensive soft tissue bone formation typical of acquired forms of heterotopic ossification (HO) and genetic bone disorders, such as Fibrodysplasia Ossificans Progressiva (FOP). Ectopic ossification in Tie2CRE/+;Bmp2tg/tg transgenic animals is accompanied by increased bone marrow hematopoietic, fibroblast and osteoblast precursors and circulating pro-inflammatory cells. Transplanting wild-type bone marrow hematopoietic stem cells into lethally irradiated Tie2CRE/+;Bmp2tg/tg mice significantly delays HO onset but does not prevent it. Moreover, transplanting Bmp2-transgenic bone marrow into wild-type recipients does not result in HO, but hematopoietic progenitors contribute to inflammation and ectopic bone marrow colonization rather than to endochondral ossification. Conversely, aberrant Bmp2 signaling activity is associated with fibroblast accumulation, skeletal muscle fiber damage, and expansion of a Tie2+ fibro-adipogenic precursor cell population, suggesting that ectopic bone derives from a skeletal muscle resident osteoprogenitor cell origin. Thus, Tie2CRE/+;Bmp2tg/tg mice recapitulate HO pathophysiology, and might represent a useful model to investigate therapies seeking to mitigate disorders associated with aberrant extra-skeletal bone formation.
The regulation of ferroptosis by MESH1 through the activation of the integrative stress response
Authors: Lin Chao-Chieh , Ding Chien-Kuang Cornelia , Sun Tianai , Wu Jianli , Chen Kai-Yuan , Zhou Pei , Chi Jen-Tsan 
Published: July 2021

AbstractAll organisms exposed to metabolic and environmental stresses have developed various stress adaptive strategies to maintain homeostasis. The main bacterial stress survival mechanism is the stringent response triggered by the accumulation “alarmone” (p)ppGpp, whose level is regulated by RelA and SpoT. While metazoan genomes encode MESH1 (Metazoan SpoT Homolog 1) with ppGpp hydrolase activity, neither ppGpp nor the stringent response is found in metazoa. The deletion of Mesh1 in Drosophila triggers a transcriptional response reminiscent of the bacterial stringent response. However, the function of MESH1 remains unknown until our recent discovery of MESH1 as the first cytosolic NADPH phosphatase that regulates ferroptosis. To further understand whether MESH1 knockdown triggers a similar transcriptional response in mammalian cells, here, we employed RNA-Seq to analyze the transcriptome response to MESH1 knockdown in human cancer cells. We find that MESH1 knockdown induced different genes involving endoplasmic reticulum (ER) stress, especially ATF3, one of the ATF4-regulated genes in the integrative stress responses (ISR). Furthermore, MESH1 knockdown increased ATF4 protein, eIF2a phosphorylation, and induction of ATF3, XBPs, and CHOP mRNA. ATF4 induction contributes to ~30% of the transcriptome induced by MESH1 knockdown. Concurrent ATF4 knockdown re-sensitizes MESH1-depleted RCC4 cells to ferroptosis, suggesting its role in the ferroptosis protection mediated by MESH1 knockdown. ATF3 induction is abolished by the concurrent knockdown of NADK, implicating a role of NADPH accumulation in the integrative stress response. Collectively, these results suggest that MESH1 depletion triggers ER stress and ISR as a part of its overall transcriptome changes to enable stress survival of cancer cells. Therefore, the phenotypic similarity of stress tolerance caused by MESH1 removal and NADPH accumulation is in part achieved by ISR to regulate ferroptosis.
Mitochondrial estrogen receptors alter mitochondrial priming and response to endocrine therapy in breast cancer cells
Authors: Karakas Bahriye , Aka Yeliz , Giray Asli , Temel Sehime Gulsun , Acikbas Ufuk , Basaga Huveyda , Gul Ozgur , Kutuk Ozgur 
Published: July 2021

AbstractBreast cancer is the most common cancer with a high rate of mortality and morbidity among women worldwide. Estrogen receptor status is an important prognostic factor and endocrine therapy is the choice of first-line treatment in ER-positive breast cancer. However, most tumors develop resistance to endocrine therapy. Here we demonstrate that BH3 profiling technology, in particular, dynamic BH3 profiling can predict the response to endocrine therapy agents as well as the development of acquired resistance in breast cancer cells independent of estrogen receptor status. Immunofluorescence analysis and subcellular fractionation experiments revealed distinct ER-α and ER-β subcellular localization patterns in breast cancer cells, including mitochondrial localization of both receptor subtypes. shRNA-mediated depletion of ER-β in breast cancer cells led to resistance to endocrine therapy agents and selective reconstitution of ER-β in mitochondria restored sensitivity. Notably, mitochondria-targeted ER-α did not restore sensitivity, even conferred further resistance to endocrine therapy agents. In addition, expressing mitochondria-targeted ER-β in breast cancer cells resulted in decreased mitochondrial respiration alongside increased total ROS and mitochondrial superoxide production. Furthermore, our data demonstrated that mitochondrial ER-β can be successfully targeted by the selective ER-β agonist Erteberel. Thus, our findings provide novel findings on mitochondrial estrogen signaling in breast cancer cells and suggest the implementation of the dynamic BH3 technique as a tool to predict acquired endocrine therapy resistance.
Machine learning based energy-free structure predictions of molecules, transition states, and solids
Authors: Lemm Dominik , von Rudorff Guido Falk , von Lilienfeld O. Anatole 
Published: July 2021

AbstractThe computational prediction of atomistic structure is a long-standing problem in physics, chemistry, materials, and biology. Conventionally, force-fields or ab initio methods determine structure through energy minimization, which is either approximate or computationally demanding. This accuracy/cost trade-off prohibits the generation of synthetic big data sets accounting for chemical space with atomistic detail. Exploiting implicit correlations among relaxed structures in training data sets, our machine learning model Graph-To-Structure (G2S) generalizes across compound space in order to infer interatomic distances for out-of-sample compounds, effectively enabling the direct reconstruction of coordinates, and thereby bypassing the conventional energy optimization task. The numerical evidence collected includes 3D coordinate predictions for organic molecules, transition states, and crystalline solids. G2S improves systematically with training set size, reaching mean absolute interatomic distance prediction errors of less than 0.2 Å for less than eight thousand training structures — on par or better than conventional structure generators. Applicability tests of G2S include successful predictions for systems which typically require manual intervention, improved initial guesses for subsequent conventional ab initio based relaxation, and input generation for subsequent use of structure based quantum machine learning models.
Decision-related feedback in visual cortex lacks spatial selectivity
Authors: Quinn Katrina R. , Seillier Lenka , Butts Daniel A. , Nienborg Hendrikje 
Published: July 2021

AbstractFeedback in the brain is thought to convey contextual information that underlies our flexibility to perform different tasks. Empirical and computational work on the visual system suggests this is achieved by targeting task-relevant neuronal subpopulations. We combine two tasks, each resulting in selective modulation by feedback, to test whether the feedback reflected the combination of both selectivities. We used visual feature-discrimination specified at one of two possible locations and uncoupled the decision formation from motor plans to report it, while recording in macaque mid-level visual areas. Here we show that although the behavior is spatially selective, using only task-relevant information, modulation by decision-related feedback is spatially unselective. Population responses reveal similar stimulus-choice alignments irrespective of stimulus relevance. The results suggest a common mechanism across tasks, independent of the spatial selectivity these tasks demand. This may reflect biological constraints and facilitate generalization across tasks. Our findings also support a previously hypothesized link between feature-based attention and decision-related activity.
Quantum gravitational decoherence from fluctuating minimal length and deformation parameter at the Planck scale
Authors: Petruzziello Luciano , Illuminati Fabrizio 
Published: July 2021

AbstractSchemes of gravitationally induced decoherence are being actively investigated as possible mechanisms for the quantum-to-classical transition. Here, we introduce a decoherence process due to quantum gravity effects. We assume a foamy quantum spacetime with a fluctuating minimal length coinciding on average with the Planck scale. Considering deformed canonical commutation relations with a fluctuating deformation parameter, we derive a Lindblad master equation that yields localization in energy space and decoherence times consistent with the currently available observational evidence. Compared to other schemes of gravitational decoherence, we find that the decoherence rate predicted by our model is extremal, being minimal in the deep quantum regime below the Planck scale and maximal in the mesoscopic regime beyond it. We discuss possible experimental tests of our model based on cavity optomechanics setups with ultracold massive molecular oscillators and we provide preliminary estimates on the values of the physical parameters needed for actual laboratory implementations.
Structure of the molecular bushing of the bacterial flagellar motor
Authors: Yamaguchi Tomoko , Makino Fumiaki , Miyata Tomoko , Minamino Tohru , Kato Takayuki , Namba Keiichi 
Published: July 2021

AbstractThe basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface.
Remote control of neural function by X-ray-induced scintillation
Authors: Matsubara Takanori , Yanagida Takayuki , Kawaguchi Noriaki , Nakano Takashi , Yoshimoto Junichiro , Sezaki Maiko , Takizawa Hitoshi , Tsunoda Satoshi P. , Horigane Shin-ichiro , Ueda Shuhei , Takemoto-Kimura Sayaka , Kandori Hideki , Yamanaka Akihiro , Yamashita Takayuki 
Published: July 2021

AbstractScintillators emit visible luminescence when irradiated with X-rays. Given the unlimited tissue penetration of X-rays, the employment of scintillators could enable remote optogenetic control of neural functions at any depth of the brain. Here we show that a yellow-emitting inorganic scintillator, Ce-doped Gd3(Al,Ga)5O12 (Ce:GAGG), can effectively activate red-shifted excitatory and inhibitory opsins, ChRmine and GtACR1, respectively. Using injectable Ce:GAGG microparticles, we successfully activated and inhibited midbrain dopamine neurons in freely moving mice by X-ray irradiation, producing bidirectional modulation of place preference behavior. Ce:GAGG microparticles are non-cytotoxic and biocompatible, allowing for chronic implantation. Pulsed X-ray irradiation at a clinical dose level is sufficient to elicit behavioral changes without reducing the number of radiosensitive cells in the brain and bone marrow. Thus, scintillator-mediated optogenetics enables minimally invasive, wireless control of cellular functions at any tissue depth in living animals, expanding X-ray applications to functional studies of biology and medicine.
S-nitrosylation-mediated coupling of G-protein alpha-2 with CXCR5 induces Hippo/YAP-dependent diabetes-accelerated atherosclerosis
Authors: Chao Meng-Lin , Luo Shanshan , Zhang Chao , Zhou Xuechun , Zhou Miao , Wang Junyan , Kong Chuiyu , Chen Jiyu , Lin Zhe , Tang Xin , Sun Shixiu , Tang Xinlong , Chen Hongshan , Wang Hong , Wang Dongjin , Sun Jin-Peng , Han Yi , Xie Liping , Ji Yong 
Published: July 2021

AbstractAtherosclerosis-associated cardiovascular disease is one of the main causes of death and disability among patients with diabetes mellitus. However, little is known about the impact of S-nitrosylation in diabetes-accelerated atherosclerosis. Here, we show increased levels of S-nitrosylation of guanine nucleotide-binding protein G(i) subunit alpha-2 (SNO-GNAI2) at Cysteine 66 in coronary artery samples from diabetic patients with atherosclerosis, consistently with results from mice. Mechanistically, SNO-GNAI2 acted by coupling with CXCR5 to dephosphorylate the Hippo pathway kinase LATS1, thereby leading to nuclear translocation of YAP and promoting an inflammatory response in endothelial cells. Furthermore, Cys-mutant GNAI2 refractory to S-nitrosylation abrogated GNAI2-CXCR5 coupling, alleviated atherosclerosis in diabetic mice, restored Hippo activity, and reduced endothelial inflammation. In addition, we showed that melatonin treatment restored endothelial function and protected against diabetes-accelerated atherosclerosis by preventing GNAI2 S-nitrosylation. In conclusion, SNO-GNAI2 drives diabetes-accelerated atherosclerosis by coupling with CXCR5 and activating YAP-dependent endothelial inflammation, and reducing SNO-GNAI2 is an efficient strategy for alleviating diabetes-accelerated atherosclerosis.
Vulnerability of the North Water ecosystem to climate change
Authors: Ribeiro Sofia , Limoges Audrey , Massé Guillaume , Johansen Kasper L. , Colgan William , Weckström Kaarina , Jackson Rebecca , Georgiadis Eleanor , Mikkelsen Naja , Kuijpers Antoon , Olsen Jesper , Olsen Steffen M. , Nissen Martin , Andersen Thorbjørn J. , Strunk Astrid , Wetterich Sebastian , Syväranta Jari , Henderson Andrew C. G. , Mackay Helen , Taipale Sami , Jeppesen Erik , Larsen Nicolaj K. , Crosta Xavier , Giraudeau Jacques , Wengrat Simone , Nuttall Mark , Grønnow Bjarne , Mosbech Anders , Davidson Thomas A. 
Published: July 2021

AbstractHigh Arctic ecosystems and Indigenous livelihoods are tightly linked and exposed to climate change, yet assessing their sensitivity requires a long-term perspective. Here, we assess the vulnerability of the North Water polynya, a unique seaice ecosystem that sustains the world’s northernmost Inuit communities and several keystone Arctic species. We reconstruct mid-to-late Holocene changes in sea ice, marine primary production, and little auk colony dynamics through multi-proxy analysis of marine and lake sediment cores. Our results suggest a productive ecosystem by 4400–4200 cal yrs b2k coincident with the arrival of the first humans in Greenland. Climate forcing during the late Holocene, leading to periods of polynya instability and marine productivity decline, is strikingly coeval with the human abandonment of Greenland from c. 2200–1200 cal yrs b2k. Our long-term perspective highlights the future decline of the North Water ecosystem, due to climate warming and changing sea-ice conditions, as an important climate change risk.
Massive carbon storage in convergent margins initiated by subduction of limestone
Authors: Chen Chunfei , Förster Michael W. , Foley Stephen F. , Liu Yongsheng 
Published: July 2021

AbstractRemobilization of sedimentary carbonate in subduction zones modulates arc volcanism emissions and thus Earth’s climate over geological timescales. Although limestones (or chalk) are thought to be the major carbon reservoir subducted to subarc depths, their fate is still unclear. Here we present high-pressure reaction experiments between impure limestone (7.4 wt.% clay) and dunite at 1.3–2.7 GPa to constrain the melting behaviour of subducted natural limestone in contact with peridotite. The results show that although clay impurities significantly depress the solidus of limestone, melting will not occur whilst limestones are still part of the subducting slab. Buoyancy calculations suggest that most of these limestones would form solid-state diapirs intruding into the mantle wedge, resulting in limited carbon flux to the deep mantle (< ~10 Mt C y−1). Less than 20% melting within the mantle wedge indicates that most limestones remain stable and are stored in subarc lithosphere, resulting in massive carbon storage in convergent margins considering their high carbon flux (~21.4 Mt C y−1). Assimilation and outgassing of these carbonates during arc magma ascent may dominate the carbon flux in volcanic arcs.
Mitochondrial transcription factor A in RORγt+ lymphocytes regulate small intestine homeostasis and metabolism
Authors: Fu Zheng , Dean Joseph W. , Xiong Lifeng , Dougherty Michael W. , Oliff Kristen N. , Chen Zong-ming E. , Jobin Christian , Garrett Timothy J. , Zhou Liang 
Published: July 2021

AbstractRORγt+lymphocytes, including interleukin 17 (IL-17)-producing gamma delta T (γδT17) cells, T helper 17 (Th17) cells, and group 3 innate lymphoid cells (ILC3s), are important immune regulators. Compared to Th17 cells and ILC3s, γδT17 cell metabolism and its role in tissue homeostasis remains poorly understood. Here, we report that the tissue milieu shapes splenic and intestinal γδT17 cell gene signatures. Conditional deletion of mitochondrial transcription factor A (Tfam) in RORγt+lymphocytes significantly affects systemic γδT17 cell maintenance and reduces ILC3s without affecting Th17 cells in the gut. In vivo deletion ofTfamin RORγt+lymphocytes, especially in γδT17 cells, results in small intestine tissue remodeling and increases small intestine length by enhancing the type 2 immune responses in mice. Moreover, these mice show dysregulation of the small intestine transcriptome and metabolism with less body weight but enhanced anti-helminth immunity. IL-22, a cytokine produced by RORγt+lymphocytes inhibits IL-13-induced tuft cell differentiation in vitro, and suppresses the tuft cell-type 2 immune circuit and small intestine lengthening in vivo, highlighting its key role in gut tissue remodeling.
Structure and function of an Arabidopsis thaliana sulfate transporter
Authors: Wang Lie , Chen Kehan , Zhou Ming 
Published: July 2021

AbstractPlant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO42−) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO42− at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO42− is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO42− are co-transported by AtSULTR4;1 and a proton gradient significantly enhances SO42− transport. Glu347, which is ~7 Å from the bound SO42−, is required for H+-driven transport. The cytosolic STAS domain interacts with transmembrane domains, and deletion of the STAS domain or mutations to the interface compromises dimer formation and reduces SO42− transport, suggesting a regulatory function of the STAS domain.