bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering T cells to enhance 3D migration through structurally and mechanically complex tumor microenvironments
Authors: Tabdanov Erdem D. , Rodríguez-Merced Nelson J. , Cartagena-Rivera Alexander X. , Puram Vikram V. , Callaway Mackenzie K. , Ensminger Ethan A. , Pomeroy Emily J. , Yamamoto Kenta , Lahr Walker S. , Webber Beau R. , Moriarity Branden S. , Zhovmer Alexander S. , Provenzano Paolo P. 
Published: April 2020

ABSTRACTDefining the principles of T cell migration in structurally and mechanically complex tumor microenvironments is critical to understanding sanctuaries from antitumor immunity and optimizing T cell-related therapeutic strategies. To enhance T cell migration through complex microenvironments, we engineered nanotextured platforms that allowed us to define how the balance between T cell phenotypes influences migration in response to tumor-mimetic structural and mechanical cues and characterize a mechanical optimum for migration that can be perturbed by manipulating an axis between microtubule stability and force generation. In 3D environments and live tumors, we demonstrate that microtubules instability, leading to increased Rho pathway-dependent cell contractility, promotes migration while clinically used microtubule-targeting chemotherapies profoundly decrease effective migration. Indeed, we show that rational manipulation of the microtubule-contractility axis, either pharmacologically or through genome engineering, results in engineered T cells that more effectively move through and interrogate 3D matrix and tumor volumes. This suggests that engineering cells to better navigate through 3D microenvironments could be part of an effective strategy to enhance efficacy of immune therapeutics.
Two novel 7-epi-zingiberene derivatives with biological activity fromSolanum habrochaitesare produced by a single cytochrome P450 monooxygenase
Authors: Zabel Sebastian , Brandt Wolfgang , Porzel Andrea , Athmer Benedikt , Kortbeek Ruy , Bleeker Petra , Tissier Alain 
Published: April 2020

AbstractSecretions from glandular trichomes potentially protect the plant against a variety of aggressors. In the tomato genus, wild species constitute a rich source of chemical diversity produced at the leaf surface by glandular trichomes. Previously, 7-epi-zingiberene produced in several accessions ofSolanum habrochaiteswas found to confer resistance to whiteflies (Bemisia tabaci) and other insect pests. Here, we identify two derivatives of 7-epi-zingiberene fromS. habrochaitesthat had not been reported as yet. We identified them as 9-hydroxy-zingiberene and 9-hydroxy-10,11-epoxyzingiberene. Using a combination of genetics and transcriptomics we identified a single cytochrome P450 oxygenase, ShCYP71D184 that carries out two successive oxidations to generate the two sesquiterpenoids. Bioactivity assays showed that only 9-hydroxy-10,11-epoxyzingiberene exhibits substantial toxicity againstB. tabaci. In addition, both 9-hydroxy-zingiberene and 9-hydroxy-10,11-epoxyzingiberene display substantial growth inhibitory activities against a range of microorganisms, includingBacillus subtilis,Phytophtora infestansandBotrytis cinerea. Our work shows that trichome secretions from wild tomato species can provide protection against a wide variety of organisms. In addition, the availability of the genes encoding the enzymes for the pathway of 7-epi-zingiberene derivatives makes it possible to introduce this trait in cultivated tomato by precision breeding.
Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma
Authors: Hayden Annette , Manousopoulou Antigoni , Cowie Andrew , Walker Robert , Sharpe Benjamin P. , Harrington Jack , Izadi Fereshteh , Kyle Ewan , Saunders John H. , Parsons Simon L. , Ritchie Alison A. , Clarke Philip A. , Collier Pamela , Garbis Spiros D. , Rose-Zerilli Matthew , Grabowska Anna M. , Underwood Timothy J. 
Published: April 2020

AbstractBackground and aimsEsophageal adenocarcinoma (EAC) is chemoresistant in the majority of cases. The tumor-promoting biology of cancer associated fibroblasts (CAF) make them a target for novel therapies. Phosphodiesterase type 5 inhibitors (PDE5i) have been shown to regulate the activated fibroblast phenotype in benign disease. We investigated the potential for CAF modulation in EAC using PDE5i to enhance the efficacy of chemotherapy.MethodsEAC fibroblasts were treated with PDE5i and phenotypic effects examined using immunoblotting, immunohistochemistry, gel contraction, transwell invasion, organotypics, single cell RNAseq and shotgun proteomics. The combination of PDE5i with standard-of-care chemotherapy (Epirubicin, 5-Fluorouracil and Cisplatin) was tested for safety and efficacy in validated near-patient model systems (3D tumor growth assays (3D-TGAs) and patient derived xenograft (PDX) mouse models).ResultsPDE5i treatment reduced α–SMA expression in CAFs by 50% (p<0.05), associated with a significant reduction in the ability of CAFs to contract collagen-1 gels and induce cancer cell invasion, (p<0.05). RNAseq and proteomic analysis of CAF and EAC cell lines revealed PDE5i specific regulation of pathways related to fibroblast activation and tumor promotion. 3D-TGA assays confirmed the importance of stromal cells to chemoresistance in EAC, which could be attenuated by PDE5i. Chemotherapy+PDE5i in PDX-bearing mice was safe and significantly reduced PDX tumor volume (p<0.05).ConclusionPDE5 is a candidate for clinical trials to alter the fibroblast phenotype in esophageal cancer. We demonstrate the specificity of PDE5i for fibroblasts to prevent transdifferentiation and revert the CAF phenotype. Finally, we confirm the efficacy of PDE5i in combination with chemotherapy in close-to-patientin vitroandin vivoPDX-based model systems.
Unveiling cells’ local environment during cryopreservation by correlativein situspatial and thermal analyses
Authors: Qin Kankan , Eschenbrenner Corentin , Ginot Felix , Dedovets Dmytro , Coradin Thibaud , Deville Sylvain , Fernandes Francisco M. 
Published: April 2020

AbstractCryopreservation is the only fully established procedure to extend the lifespan of living cells and tissues, a key to activities spanning from fundamental biology to clinical practice. Despite its prevalence and impact, central aspects of cryopreservation, such as the cell’s physico-chemical environment during freezing, remain elusive. Here we address that question by couplingin situmicroscopic directional freezing to visualize cells and their surroundings during freezing with the freezing medium phase diagram. We extract the freezing medium spatial distribution in cryopreservation, providing a tool to describe the cell vicinity at any point during freezing. We show that two major events define the cells’ local environment over time: the interaction with the moving ice front and with the vitreous moving front – a term we introduce here. Our correlative strategy may be applied to cells relevant in clinical research and practice, and help designing new cryoprotective media based on local physico-chemical cues.
K-means Based Unsupervised Feature Selection to Prioritize Biomarkers of Different Disease Clinical Phases
Authors: Jiang Xue , Wang Weidi , Xu Jing , Wang Zhen , Lin Guan Ning 
Published: April 2020

AbstractHuntington’s disease is caused by a single gene mutation, which is potentially a good model for development of biomarkers corresponding to different disease phase and clinical phenotypes. Hypothesis-driven and omics discovery approaches have not yet identified effective candidate biomarkers in HD. So, it is urgent to develop engagement and disease-phase specific biomarkers. The advanced sequencing technology makes it possible to develop data-driven methods for biomarkers discovery. Therefore, in this study, we designed k-means based unsupervised feature selection (KFS) method to prioritize biomarkers of different disease clinical phases. KFS first conducts k-means clustering on the samples with gene expression data, then it conducts feature selection based on the feature selection matrix to prioritize biomarkers of different samples. By conducting alternative iteration of clustering and feature selection to screen key genes which corresponding to the complex clinical phenotypes of different disease phases. Further gene ontology and enrichment analysis highlight potential molecular mechanisms of HD. Our experimental analyses have uncovered new disease-related genes and disease-associated pathways, which in turn have provided insight into the molecular mechanisms during the disease progression.
Open database searching enables the identification and comparison of bacterial glycoproteomes without defining glycan compositions prior to searching
Authors: Izaham Ameera Raudah Ahmad , Scott Nichollas E. 
Published: April 2020

ABSTRACTMass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. While glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach usingN-linked glycopeptides ofCampylobacter fetus subsp. fetusas well asO-linked glycopeptides ofAcinetobacter baumanniiandBurkholderia cenocepaciarevealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses prior to database searching. Utilising this approach, we demonstrate how wide tolerance searching can be used to compare glycan utilisation across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.
Nicotinamide promotes differentiation of pancreatic endocrine progenitors from human pluripotent stem cells through poly (ADP-ribose) polymerase inhibition
Authors: Woodford Curtis , Yin Ting , Chang Huntley H , Regeenes Romario , Vellanki Ravi N , Mohan Haneesha , Wouters Bradly G , Rocheleau Jonathan V , Wheeler Michael B , Zandstra Peter W 
Published: April 2020

AbstractThe generation of pancreatic endocrine progenitor cells is an important step in the differentiation of beta cells from human pluripotent stem cells (hPSC). This stage is marked by the expression of Nkx6.1, a transcription factor with well understood downstream targets but with unclear upstream regulators. In hPSC differentiation, Nkx6.1 is strongly induced by nicotinamide, a derivative of vitamin B3, which has three known functions within a cell. Nicotinamide inhibits two classes of enzymes known as poly-ADP-ribose polymerases (PARPs) and sirtuins. It also contributes to the cellular pool of nicotinamide adenosine deoxynucleotide (NAD+) after conversion in the nicotinamide salvage pathway. Induction of Nkx6.1 expression in pancreatic endocrine progenitors by nicotinamide was mimicked by 3 PARP inhibitors (PJ34, olaparib, NU1025). Small molecule inhibition of the nicotinamide salvage pathway reduced Nkx6.1 expression but not Pdx1 expression and caused alteration in NAD+/NADH ratio. Nkx6.1 expression was not affected by sirtuin inhibition. Metabolic profiling of differentiating pancreatic and endocrine progenitors showed that oxygen consumption increases as differentiation progresses, and that nicotinamide reduces oxygen consumption rate. Expression of Nkx6.1 and other beta cell related genes, including Ins2 and Pdx1 increased in mouse islets after exposure to nicotinamide. In summary, nicotinamide induced Nkx6.1 expression in differentiating human pancreatic endocrine progenitors through inhibition of the PARP family of enzymes. Nicotinamide administration was also associated with increased NAD+/NADH ratio, without affecting Nkx6.1 expression. Similarly, the association between nicotinamide and Nkx6.1 expression was also seen in isolated mouse islets. These observations show a link between the regulation of beta cell identity and the effectors of NAD+metabolism, suggesting possible therapeutic targets in the field of diabetes.
A general 3D model for growth dynamics of sensory-growth systems: from plants to robotics
Authors: Porat Amir , Tedone Fabio , Palladino Michele , Marcati Pierangelo , Meroz Yasmine 
Published: April 2020

ABSTRACTIn recent years there has been a rise in interest in the development of self-growing robotics inspired by the moving-by-growing paradigm of plants. In particular, climbing plants capitalize on their slender structures to successfully negotiate unstructured environments, while employing a combination of two classes of growth-driven movements: tropic responses, which direct growth in the direction of an external stimulus, and inherent nastic movements, such as periodic circumnutations, which promote exploration. In order to emulate these complex growth dynamics in a 3D environment, a general and rigorous mathematical framework is required. Here we develop a general 3D model for rod-like organs adopting the Frenet-Serret frame, providing a useful framework from the standpoint of robotics control. Differential growth drives the dynamics of the organ, governed by both internal and external cues. We describe the numerical method required to implement this model, and perform numerical simulations of a number of key scenarios, showcasing the applicability of our model. In the case of responses to external stimuli, we consider a distant stimulus (such as sunlight and gravity), a point stimulus (a point light source), and a line stimulus which emulates twining of a climbing plant around a support. We also simulate circumnutations, the response to an internal oscillatory cue, associated with search processes. Lastly we also demonstrate the superposition of both the response to an external stimulus together with circumnutations. Lastly we consider a simple example illustrating the possible use of an optimal control approach in order to recover tropic dynamics, in a way which may be relevant for robotics use. In all, the model presented here is general and robust, paving the way for a deeper understanding of plant response dynamics, as well as novel control systems for newly developed self-growing robots.
Neural Signatures of α2 Adrenergic Agonist-Induced Unconsciousness and Awakening by Antagonist
Authors: Ballesteros Jesus J. , Briscoe Jessica , Ishizawa Yumiko 
Published: April 2020

AbstractHow the brain dynamics transition during anesthetic-induced altered states of consciousness is not completely understood. Theα2 adrenergic agonist is a unique anesthetic that generates unconsciousness selectively throughα2 adrenergic receptors and related circuits. We studied intracortical neuronal dynamics during transitions of loss of consciousness (LOC) with theα2 adrenergic agonist dexmedetomidine and return of consciousness (ROC) in a functionally interconnecting somatosensory and ventral premotor network in non-human primates. LOC, ROC and full task performance recovery were all associated with distinct neural changes. The early recovery demonstrated characteristic intermediate dynamics distinguished by sustained high spindle activities. Awakening by theα2 adrenergic antagonist completely eliminated this intermediate state and instantaneously restored awake dynamics and the top task performance while the anesthetic was still being infused. The results suggest that instantaneous functional recovery is possible following anesthetic-induced unconsciousness and the intermediate recovery state is not a necessary path for the brain recovery.
Enteroendocrine cells couple nutrient sensing to nutrient absorption by regulating ion transport
Authors: McCauley Heather A. , Matthis Andrea L. , Enriquez Jacob R. , Nichol Jonah , Sanchez J. Guillermo , Stone William J. , Sundaram Nambirajan , Helmrath Michael A. , Montrose Marshall H. , Aihara Eitaro , Wells James M. 
Published: April 2020

SummaryThe ability to absorb ingested nutrients is an essential function of all metazoans and utilizes a wide array of nutrient transporters found on the absorptive enterocytes of the small intestine. A unique population of patients has previously been identified with severe congenital malabsorptive diarrhea upon ingestion of any enteral nutrition. The intestines of these patients are macroscopically normal, but lack enteroendocrine cells (EECs), suggesting an essential role for this rare population of nutrient-sensing cells in regulating macronutrient absorption. We used human and mouse models of EEC deficiency to identify a new role for the EEC hormone peptide YY in regulating ion-coupled absorption of glucose and dipeptides the small intestine. We found that peptide YY is required in to maintain normal electrophysiology in the presence of vasoactive intestinal polypeptide, a potent stimulator of ion secretion produced by enteric neurons. Administration of peptide YY to EEC-deficient mice restored normal electrophysiology, improved glucose and peptide absorption, diminished diarrhea and rescued postnatal survival. These data suggest that peptide YY is a key regulator of macronutrient absorption in the small intestine and may be a viable therapeutic option to treat patients with malabsorption.
Ligand-directed covalent labelling of a GPCR with a fluorescent tag
Authors: Stoddart Leigh A , Kindon Nicholas D , Otun Omolade , Harwood Clare R. , Patera Foteini , Veprintsev Dmitry B , Woolard Jeanette , Briddon Stephen J , Franks Hester A , Hill Stephen J , Kellam Barrie 
Published: April 2020

AbstractHere, we describe rational design of a compound that covalently and selectively labels a G protein-coupled receptor (GPCR) in living cells with a fluorescent moiety. Using wild-type adenosine A2Areceptor as a model system, we show fluorescent labelling without impeding access to the orthosteric binding site and demonstrate its use in endogenously expressing systems. This offers a non-invasive and selective approach to study function and localisation of native GPCRs.
The relationship of mRNA with protein expression in CD8+T cells associates with gene class and gene characteristics
Authors: Nicolet Benoît P. , Wolkers Monika C. 
Published: April 2020

SUMMARYT cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and massspectrometry data of primary human CD8+T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3’UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.
CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species
Authors: Lee John , Shah Manthan , Ballouz Sara , Crow Megan , Gillis Jesse 
Published: April 2020

ABSTRACTCo-expression analysis has provided insight into gene function in organisms from Arabidopsis to Zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties, or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifyingconserved gene modules andcomparingco-expressionnetworks. CoCoCoNet is a resource for both data and methods, providing gold-standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups, and translated to model organisms. CoCoCoNet is free to use and available to all athttps://milton.cshl.edu/CoCoCoNet, with data and R scripts available atftp://milton.cshl.edu/data.
Population genomics insights into the recent evolution of SARS-CoV-2
Authors: Vasilarou Maria , Alachiotis Nikolaos , Garefalaki Joanna , Beloukas Apostolos , Pavlidis Pavlos 
Published: April 2020

AbstractThe current coronavirus disease 2019 (COVID-19) pandemic is caused by the SARS-CoV-2 virus and is still spreading rapidly worldwide. Full-genome-sequence computational analysis of the SARS-CoV-2 genome will allow us to understand the recent evolutionary events and adaptability mechanisms more accurately, as there is still neither effective therapeutic nor prophylactic strategy. In this study, we used population genetics analysis to infer the mutation rate and plausible recombination events that may have contributed to the evolution of the SARS-CoV-2 virus. Furthermore, we localized targets of recent and strong positive selection. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from non-human hosts appeared to have taken place in the past. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., Hedgehog and Sparrow. Even though recombination events within human hosts cannot be directly assessed, due to the high similarity of SARS-CoV-2 genomes, we infer that recombinations may have recently occurred within human hosts using a linkage disequilibrium analysis. In addition, we employed an Approximate Bayesian Computation approach to estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian and Northern American cohorts, and we demonstrated that a rapid exponential growth in population size can support the observed polymorphism patterns in SARS-CoV-2 genomes.