bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome profiling of the branchial arches reveals cell type composition and a conserved signature of neural crest cell invasion
Authors: Morrison Jason A , McLennan Rebecca , Teddy Jessica M , Scott Allison R , Kasemeier-Kulesa Jennifer C , Gogol Madelaine M , Kulesa Paul M 
Published: February 2020

ABSTRACTThe vertebrate branchial arches that give rise to structures of the head, neck, and heart form with very dynamic tissue growth and well-choreographed neural crest, ectoderm, and mesoderm cell dynamics. Although this morphogenesis has been studied by marker expression and fate-mapping, the mechanisms that control the collective migration and diversity of the neural crest and surrounding tissues remain unclear, in part due to the effects of averaging and need for cell isolation in conventional transcriptome analysis experiments of multiple cell populations. We used label free single cell RNA sequencing on 95,000 individual cells at 2 developmental stages encompassing formation of the first four chick branchial arches to measure the transcriptional states that define the cellular hierarchy and invasion signature of the migrating neural crest. The results confirmed basic features of cell type diversity and led to the discovery of many novel markers that discriminate between axial level and distal-to-proximal cell populations within the branchial arches and neural crest streams. We identified the transcriptional signature of the most invasive neural crest that is conserved within each branchial arch stream and elucidated a set of genes common to other cell invasion signatures in types in cancer, wound healing and development. These data robustly delineate molecularly distinct cell types within the branchial arches and identify important molecular transitions within the migrating neural crest during development.
In-cell architecture of an actively transcribing-translating expressome
Authors: O’Reilly Francis J. , Xue Liang , Graziadei Andrea , Sinn Ludwig , Lenz Swantje , Tegunov Dimitry , Blötz Cedric , Hagen Wim J. H. , Cramer Patrick , Stülke Jörg , Mahamid Julia , Rappsilber Juri 
Published: February 2020

AbstractStructural biology performed inside cells can capture molecular machines in action within their native context. Here we develop an integrative in-cell structural approach using the genome-reduced human pathogenMycoplasma pneumoniae. We combine whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpoint NusA at the interface between a NusG-bound elongating RNAP and the ribosome, and propose it could mediate transcription-translation coupling. Translation inhibition dissociates the expressome, whereas transcription inhibition stalls and rearranges it, demonstrating that the active expressome architecture requires both translation and transcription elongation within the cell.
GOT1 Inhibition Primes Pancreatic Cancer for Ferroptosis through the Autophagic Release of Labile Iron
Authors: Kremer Daniel M. , Nelson Barbara S. , Lin Lin , Yarosz Emily L. , Halbrook Christopher J. , Kerk Samuel A. , Sajjakulnukit Peter , Myers Amy , Thurston Galloway , Hou Sean W. , Carpenter Eileen S. , Andren Anthony C. , Nwosu Zeribe C. , Cusmano Nicholas , Wisner Stephanie , Ramos Johanna , Gao Tina , Sastra Stephen A. , Palermo Carmine F. , Badgley Michael A. , Zhang Li , Asara John M. , di Magliano Marina Pasca , Shah Yatrik M. , Crawford Howard C. , Olive Kenneth P. , Lyssiotis Costas A. 
Published: March 2020

SummaryPancreatic ductal adenocarcinoma (PDA) is one of the deadliest solid malignancies, with a 5-year survival rate at ten percent. PDA have unique metabolic adaptations in response to cell-intrinsic and environmental stressors, and identifying new strategies to target these adaptions is an area of active research. We previously described a dependency on a cytosolic aspartate aminotransaminase (GOT1)-dependent pathway for NADPH generation. Here, we sought to identify metabolic dependencies induced by GOT1 inhibition that could be exploited to selectively kill PDA. Using pharmacological methods, we identified cysteine, glutathione, and lipid antioxidant function as metabolic vulnerabilities following GOT1 withdrawal. Targeting any of these pathways was synthetic lethal in GOT1 knockdown cells and triggered ferroptosis, an oxidative, non-apoptotic, iron-dependent form of cell death. Mechanistically, GOT1 inhibition promoted the activation of autophagy in response to metabolic stress. This enhanced the availability of labile iron through ferritinophagy, the autolysosome-mediated degradation of ferritin. In sum, our study identifies a novel biochemical connection between GOT1, iron regulation, and ferroptosis, and suggests the rewired malate-aspartate shuttle plays a role in protecting PDA from severe oxidative challenge.HighlightsPDA exhibit varying dependence on GOT1 forin vitroandin vivogrowth.Exogenous cystine, glutathione synthesis, and lipid antioxidant fidelity are essential under GOT1 suppression.GOT1 inhibition sensitizes pancreatic cancer cell lines to ferroptosis.GOT1 inhibition represses anabolic metabolism and promotes the release of iron through autophagy.
MiR-101a loaded Extracellular Nanovesicles as Bioactive Carriers for Cardiac Repair
Authors: Wang Jinli , Lee Christine J. , Deci Michael B. , Jasiewicz Natalie , Canty John M , Nguyen J. 
Published: February 2020

AbstractMyocardial infarction (MI) remains a major cause of mortality worldwide. Despite significant advances in MI treatment, many who survive the acute event are at high risk of chronic cardiac morbidity. Here we developed a cell-free therapeutic that capitalizes on the antifibrotic effects of micro(mi)RNA-101a and exploits the multi-faceted regenerative activity of mesenchymal stem cell (MSC) extracellular nanovesicles (eNVs). While the majority of MSC eNVs require local delivery via intramyocardial injection to exert therapeutic efficacy, we have developed MSC eNVs that can be administered in a minimally invasive manner, all while remaining therapeutically active. When loaded with miR-101a, MSC eNVs substantially decreased infarct size (12 ± 2.4% vs. 21.4 ± 5.7%) and increased ejection fraction (53.6 ± 7.6% vs. 40.3 ± 6.0%) and fractional shortening (23.6 ± 4.3% vs. 16.6 ± 3.0%) compared to control. These findings are significant as they represent an advance in the development of minimally invasive cardio-therapies.
Picomolar affinity antagonist and sustained signaling agonist peptide ligands for the adrenomedullin and calcitonin gene-related peptide receptors
Authors: Booe Jason M. , Warner Margaret L. , Pioszak Augen A. 
Published: February 2020

AbstractThe calcitonin receptor-like G protein-coupled receptor (CLR) mediates adrenomedullin (AM) and calcitonin gene-related peptide (CGRP) actions including vasodilation, cardioprotection, and nociception. Receptor activity-modifying proteins (RAMP1-3) determine CLR ligand selectivity through an unresolved mechanism. CLR-RAMP complexes are drug targets, but short AM and CGRP plasma half-lives limit their therapeutic utility. We used combinatorial peptide library and rational design approaches to probe selectivity determinants and develop short AM and CGRP variants with ∼1000-fold increased receptor extracellular domain affinities. Binding and structural studies explained the increased affinities and defined roles for AM Lys46 and RAMP modulation of CLR conformation in selectivity. In longer scaffolds that also bind the CLR transmembrane domain the variants generated picomolar affinity antagonists, one with an estimated 12.5 hr CGRP receptor residence time, andsustainedsignaling agonists ss-AM and ss-CGRP. This work clarifies the RAMP-modulated ligand selectivity mechanism and provides AM and CGRP variants with promise as long-acting therapeutics.
Cumulus cell acetyl-CoA metabolism from acetate is associated with maternal age but inconclusively with oocyte maturity
Authors: Anderson Sharon , Xu Peining , Frey Alexander J. , Goodspeed Jason R. , Doan Mary T. , Orris John J. , Clements Nicolle , Glassner Michael J. , Snyder Nathaniel W. 
Published: February 2020

AbstractCumulus cell (CC) clumps that associate with oocytes provide the oocytes with growth and signaling factors. Thus, the metabolism of the CCs may influence oocyte function and CC metabolism may be predictive of oocyte competence for in vitro fertilization. CCs are thought to be highly glycolytic but data on other potential carbon substrates are lacking in humans. This was a prospective and blinded cohort study that was designed to examine the substrate utilization of CCs by age and oocyte competence. Individual sets of CC clumps from participants were removed after oocyte retrieval procedure, incubated with stable isotope labeled substrates, and analyzed using liquid chromatography-high resolution mass spectrometry (LC-HRMS) for isotopologue enrichment of major metabolic intermediates, including acetyl-CoA. The acyl-chain of acetyl-CoA contains 2 carbons that can be derived from13C-labeled substrates resulting in a M+2 isotopologue that contains 213C atoms. Comparing the fate of three major carbon sources, mean enrichment of M+2 acetyl-CoA (mean, standard deviation) was for glucose (3.6, 7.7), for glutamine (9.4, 6.2), and for acetate (20.7, 13.9). Due to this unexpected high and variable labeling from acetate, we then examined acetyl-CoA mean % enrichment from acetate of in 278 CCs from 21 women ≤34 (49.06, 12.73) decreased with age compared to 124 CCs from 10 women >34 (43.48, 16.20) (p=0.0004, t test). The CCs associated with the immature prophase I oocytes had significantly lower enrichment in M+2 acetyl CoA compared to the CCs associated with the metaphase I and metaphase II oocytes (difference: −6.02, CI: −1.74,-13.79, p=0.013). Acetate metabolism in individual CC clumps was positively correlated with oocyte maturity and decreased with maternal age. These findings indicate that CC metabolism of non-glucose substrates should be investigated relative to oocyte function and age-related fertility.
Tissue-resident CD4+T helper cells assist protective respiratory mucosal B and CD8+T cell memory responses
Authors: Son Young Min , Cheon In Su , Wu Yue , Li Chaofan , Wang Zheng , Chen Yao , Takahashi Yoshimasa , Dent Alexander L. , Kaplan Mark H , Fu Yang-Xin , Taylor Justin J. , Cui Weiguo , Sun Jie 
Published: February 2020

AbstractThe roles of CD4+T helper cells (TH) in shaping localized memory B and CD8+T cell immunity in the mucosal tissues are largely unexplored. Here, we report that lung THcells provide local assistance for the optimal development of tissue-resident memory B (BRM) and CD8+T (TRM) cells following the resolution of primary influenza virus infection. We identify a population of tissue-resident CD4+TH(akaTRH) cells that co-exhibit follicular T helper (TFH) and TRMcell features and mediate local help of CD4+T cells to B and CD8+T cells. Optimal TRHcell formation requires lung B cells and transcription factors involved in TFHor TRMdevelopment. Further, we show that TRHcells deliver local help to B and CD8 T cells through CD40L and IL-21-dependent mechanisms. Our data have uncovered a new tissue-resident THcell population that is specialized in assisting the development of mucosal protective B and CD8+T cell responsesin situ.
Size-dependent patterns of cell proliferation and migration in freely-expanding epithelia
Authors: Heinrich Matthew A. , Alert Ricard , LaChance Julienne M. , Zajdel Tom J. , Košmrlj Andrej , Cohen Daniel J. 
Published: February 2020

AbstractThe coordination of cell proliferation and migration in growing tissues is crucial in development and regeneration but remains poorly understood. Here, we find that, while expanding with an edge speed independent of initial conditions, millimeter-scale epithelial monolayers exhibit internal patterns of proliferation and migration that depend not on the current but on the initial tissue size, indicating memory effects. Specifically, the core of large tissues becomes very dense, almost quiescent, and ceases cell-cycle progression. In contrast, initially-smaller tissues develop a local minimum of cell density and a tissue-spanning vortex. To explain vortex formation, we propose an active polar fluid model with a feedback between cell polarization and tissue flow. Taken together, our findings suggest that expanding epithelia decouple their internal and edge regions, which enables robust expansion dynamics despite the presence of size- and history-dependent patterns in the tissue interior.
Three-dimensional reconstruction of individual helical nano-filament structures from atomic force microscopy topographs
Authors: Lutter Liisa , Serpell Christopher , Tuite Mick , Serpell Louise , Xue Wei-Feng 
Published: February 2020

ABSTRACTAtomic force microscopy, AFM, is a powerful tool that can produce detailed topographical images of individual nano-structures with a high signal-to-noise ratio without the need for ensemble averaging. However, the application of AFM in structural biology has been hampered by the tip-sample convolution effect, which distorts images of nano-structures, particularly those that are of similar dimensions to the cantilever probe tips used in AFM. Here we show that the tip-sample convolution results in a feature-dependent and non-uniform distribution of image resolution on AFM topographs. We show how this effect can be utilised in structural studies of nano-sized upward convex objects such as spherical or filamentous molecular assemblies deposited on a flat surface, because it causes ‘magnification’ of such objects in AFM topographs. Subsequently, this enhancement effect is harnessed through contact-point based deconvolution of AFM topographs. Here, the application of this approach is demonstrated through the 3D reconstruction of the surface envelope of individual helical amyloid filaments without the need of cross-particle averaging using the contact-deconvoluted AFM topographs. Resolving the structural variations of individual macromolecular assemblies within inherently heterogeneous populations is paramount for mechanistic understanding of many biological phenomena such as amyloid toxicity and prion strains. The approach presented here will also facilitate the use of AFM for high-resolution structural studies and integrative structural biology analysis of single molecular assemblies.
Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods
Authors: Robinson Chloe V. , Porter Teresita M. , Wright Michael T.G. , Hajibabaei Mehrdad 
Published: February 2020

AbstractMaintaining the integrity of DNA in bulk environmental samples from source to laboratory is crucial for capturing the true range of taxa present within an ecosystem. Preservation consideration of DNA is particularly important if samples are being collected in remote areas and by non-specialist ‘citizen scientists’ in nationwide programs. Traditionally, absolute ethanol is used as the preferred preservative for environmental samples collected for downstream DNA metabarcoding analyses. However, transport, shipping and DNA extraction of samples preserved in ethanol is a lengthy procedure due to safety restrictions and the requirement of full ethanol evaporation prior to extraction. We examined the efficacy of an easily accessible, non-toxic propylene glycol-based antifreeze as an alternative to absolute ethanol for preserving macroinvertebrate DNA from bulk-benthos DNA samples. We tested the differences in both cytochrome oxidase I (COI) exact sequence variants (ESVs) and COI taxonomic orders detected in both ethanol and antifreeze samples using two processing methods (no evaporation of preservative versus full evaporation). In addition, we assessed the detection of families and genera within the Arthropoda phylum for preservative type, site and processing method. Our results suggest that antifreeze is a suitable alternative to ethanol, a greater global ESV richness reported for antifreeze samples. Additionally, a higher proportion of arthropod reads in ESVs were detected in antifreeze (average 69%) compared with ethanol (average 53%). Finally, antifreeze samples produced similar results for the different processing methods, whereas ethanol samples failed to produce similar results without prior evaporation. Although ethanol is currently widely used for DNA preservation, our results demonstrate that by using antifreeze, it is possible to achieve similar taxonomic coverage and community assemblages of bulk-benthos DNA samples for macroinvertebrates, with the added simplicity and shorter laboratory processing time achieved using an easily available, unregulated preservative.
Loops and the activity of loop extrusion factors constrain chromatin dynamics
Authors: Bailey Mary Lou P. , Surovtsev Ivan , Williams Jessica F. , Yan Hao , Yuan Tianyu , Li Kevin , Duseau Katherine , Mochrie Simon G. J. , King Megan C. 
Published: March 2020

AbstractThe chromosomes - DNA polymers and their binding proteins - are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood. To gain insight into the structure-dynamics relationship of chromatin, we combine high-precision microscopy in livingSchizosaccharomyces pombecells with systematic genetic perturbations and Rouse- model polymer simulations. We first investigated how the activity of two loop extrusion factors, the cohesin and condensin complexes, influences chromatin dynamics. We observed that deactivating cohesin, or to a lesser extent condensin, increased chromatin mobility, suggesting that loop extrusion constrains rather than agitates chromatin motion. Our corresponding simulations reveal that the introduction of loops is sufficient to explain the constraining activity of loop extrusion factors, highlighting that the conformation adopted by the polymer plays a key role in defining its dynamics. Moreover, we find that the number loops or residence times of loop extrusion factors influences the dynamic behavior of the chromatin polymer. Last, we observe that the activity of the INO80 chromatin remodeler, but not the SWI/SNF or RSC complexes, is critical for ATP-dependent chromatin mobility in fission yeast. Taken together we suggest that thermal and INO80-dependent activities exert forces that drive chromatin fluctuations, which are constrained by the organization of the chromosome into loops.
The potentiation of menadione on imatinib by downregulation of ABCB1 expression
Authors: Xiao Fei‐Yan , Zhou Fang‐Jiao , Yuan Fang , Kuang Wei , Zhou Gan , Zhou Hong‐Hao , Cao Shan 
Published: February 2020

AbstractImatinib was the first BCR‐ABL inhibitor used in clinical practice to treat chronic myeloid leukaemia (CML) and significantly improve the life expectancy of CML patients in the chronic phase. However, a portion of CML patients are resistant to imatinib. This study aimed to determine whether menadione (Vitamin K3) can improve imatinib efficacy in CML and to thoroughly explore the combination regimen mechanism between imatinib and menadione. Menadione improved imatinib efficacy in K562 cells by downregulating ABCB1 expression and increased the intracellular concentration of imatinib, which confirmed that this combination regimen is more effective than imatinib monotherapy. The results demonstrate that menadione and imatinib combination therapy may be a promising approach to refractory CML.
Interprofessional partnerships involving school counsellors for children with special needs: a broad based systematic review using the PRISMA framework
Authors: Johnson Kaprea F. , Belcher T’Airra W. , Zimmerman Betsy , Franklin Jeanel 
Published: February 2020

AbstractInterprofessional educational partnerships can include a diverse group of helping professionals involved in consultation at both the school and community levels. Central to these partnerships should be school counsellors; this systematic review sought to understand the dynamics of these partnerships using the PRISMA framework. The review found that the role school counsellors can play on these teams varies from leader to convener but the specificity in terms of outcomes was missing. Noteworthy is the number of conceptual pieces, which is interpreted as researchers developing models that need additional testing. Future research should put the conceptual models available to directional testing; authors should include more information about the team’s development and each person’s role; and more attention should be paid to the outcomes of these team‐based approaches.
Closing the gap: supporting literacy through a computer‐assisted‐reading‐intervention
Authors: Vincent Kerry 
Published: February 2020

AbstractSchools in England are expected to ‘close the gap’ for a range of vulnerable pupils who are achieving below the levels seen amongst their same‐aged peers. They are also highly accountable for additional funding that is provided to support this goal. The project reported here involved collating and analysing a range of data in order to evaluate the impact of a widely used computer‐assisted‐reading‐intervention (CARI). Sixteen primary school pupils, all of whom were identified by their school as underachieving in literacy, used the CARI daily over a five‐week period. The post‐intervention data showed some clear gains in reading and spelling skills for all bar one of the children. The findings are discussed in relation to the wider literatures on CARIs. The research concludes that the CARI under investigation offers a useful and cost‐effective adjunct to whole‐class and group reading instruction and may be particularly beneficial for supporting the learning of pupils who are struggling to consolidate the knowledge and skills covered in their regular classroom reading instruction.
Pupil participation in planning provision for special educational needs: teacher perspectives
Authors: Merrick Rosalind 
Published: February 2020

AbstractThere are legal, moral and practical reasons to involve pupils in planning provision for their special educational needs. We do not yet know how principles are implemented in practice. This study explored the views and experiences of 64 teachers with an interest in special educational needs through an online survey. Participants reported greater pupil involvement in everyday matters, less in conceptual aspects of planning. Effective strategies were based on good teacher‐pupil relationships and school‐wide systems for sharing pupil views. Participants gave examples of the impact of pupil participation on teacher insight, pupil motivation and material provision. 84 per cent indicated that they would like pupils to be more involved in decisions about their provision than they currently are. Barriers included the nature of children’s difficulties and practitioner attitudes. Listening to children is intrinsic to good teaching, yet pupils also benefit from a more formal role in provision planning.