bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of immunoactive and immunotolerant CD4+ T cells in breast cancer by measuring activity of signaling pathways that determine immune cell function
Authors: Wesseling-Rozendaal Yvonne , van Doorn Arie , Willard-Gallo Karen , van de Stolpe Anja 
Published: October 2020

AbstractCancer immunotolerance can be reversed by checkpoint blockade immunotherapy in some patients, but response prediction remains a challenge. CD4+ T cells play an important role in activating adaptive immune responses against cancer. Conversion to an immune suppressive state impairs the anti-cancer immune response and is mainly effected by CD4+ Treg cells. A number of signal transduction pathways activate and control functions of CD4+ T cell subsets. As previously described, assays have been developed which enable quantitative measurement of the activity of signal transduction pathways (e.g. TGFβ, NFκB, PI3K-FOXO, JAK-STAT1/2, JAK-STAT3, Notch) in a cell or tissue sample. Using these assays, pathway activity profiles for various CD4+ T cell subsets were defined and cellular mechanisms underlying breast cancer-induced immunotolerance investigatedin vitro. Results were used to measure the immune response state in a clinical breast cancer study.MethodsSignal transduction pathway activity scores were measured on Affymetrix expression microarray data of resting and immune-activated CD4+ T cells, immune-activated CD4+ T cells incubated with breast cancer tissue supernatants, CD4+ Th1, Th2, and Treg cells, and of clinical study samples in which CD4+ T cells were derived from blood, lymph node and cancer tissue from primary breast cancer patients (n=10).ResultsIn vitroCD4+ T cell activation induced PI3K, NFκB, JAK-STAT1/2, and JAK-STAT3 pathway activity. Simultaneous incubation with primary cancer supernatant reduced PI3K and NFκB, and partly reduced JAK-STAT3, pathway activity, while simultaneously increasing TGFβ pathway activity; characteristic of an immune tolerant state. CD4+ Th1, Th2, and Treg cells all had a specific pathway activity profile, with activated immune suppressive Treg cells characterized by high NFκB, JAK-STAT3, TGFβ, and Notch pathway activity scores. An immune tolerant pathway profile was identified in CD4+ T cells from tumor infiltrate of a subset of primary breast cancer patients which could be contributed to activated Treg cells. A Treg pathway profile was also identified in blood samples.ConclusionSignaling pathway assays can be used to quantitatively measure the functional immune response state of lymphocyte subsetsin vitroandin vivo. Clinical results suggest that in primary breast cancer the adaptive immune response of CD4+ T cells has frequently been replaced by immunosuppressive Treg cells, potentially causing resistance to checkpoint inhibition.In vitrostudy results suggest that this effect is mediated by soluble factors from cancer tissue (e.g. TGFβ). Signaling pathway activity analysis on TIL and/or blood samples is expected to improve predicting and monitoring response to checkpoint inhibitor immunotherapy.
Discriminative SKP2 interactions with CDK-cyclin complexes support a cyclin A-specific role in p27KIP1 degradation
Authors: Salamina Marco , Montefiore Bailey C. , Liu Mengxi , Wood Daniel J. , Heath Richard , Ault James R. , Wang Lan-Zhen , Korolchuk Svitlana , Baslé Arnaud , Pastok Martyna W. , Reeks Judith , Tatum Natalie J. , Sobott Frank , Arold Stefan T. , Pagano Michele , Noble Martin E.M. , Endicott Jane A. 
Published: October 2020

AbstractThe SCFSKP2ubiquitin ligase relieves G1 checkpoint control of CDK-cyclin complexes by promoting p27KIP1 degradation. We describe reconstitution of stable complexes containing SKP1-SKP2 and CDK1-cyclin B or CDK2-cyclin A/E, mediated by the CDK regulatory subunit CKS1. We further show that a direct interaction between a SKP2 N-terminal motif and cyclin A can stabilize SKP1-SKP2-CDK2-cyclin A complexes in the absence of CKS1. We identify the SKP2 binding site on cyclin A and demonstrate the site is not present in cyclin B or cyclin E. This site is distinct from but overlapping with features that mediate binding of p27KIP1 and other G1 cyclin regulators to cyclin A. We propose that the capacity of SKP2 to engage with CDK2-cyclin A by more than one structural mechanism provides a way to fine tune the degradation of p27KIP1 and distinguishes cyclin A from other G1 cyclins to ensure orderly cell cycle progression.
Simulation-guided engineering of antibiotics for improved bacterial uptake
Authors: Ferreira Ricardo J. , Aguilar Valeria , Villamil Giraldo Ana M. , Kasson Peter M. 
Published: October 2020

AbstractThe Gram-negative bacterial outer membrane poses a major obstacle to the development of much-needed antibiotics against drug-resistant infections. Its chemical composition and porin proteins differ from Gram-positive bacteria and mammalian cells, and heuristics developed for mammalian cell uptake apply poorly. Recently, machinelearning methods have predicted small-molecule uptake into Gram-negative bacteria, offering the possibility to rationally optimize this aspect of antibiotic lead development. Here, we report physics-based methods to prospectively predict Gram-negative bacterial uptake, select, and synthesize promising chemical derivatives targetingE. coliDNA gyrase B. Our methods do not require empirical parameterization and are readily adaptable to new chemical scaffolds. These physics-based predictions well capture experimentally measured uptake (r > 0.95) and are indeed predictive of antimicrobial activity (r > 0.92). These methods can be used prospectively in combination with target-binding simulations to optimize both bacterial uptake and target binding, overcoming important barriers to antibiotic lead generation before small-molecule synthesis.
CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation
Authors: Kared Hassen , Redd Andrew D , Bloch Evan M , Bonny Tania S. , Sumatoh Hermi , Kairi Faris , Carbajo Daniel , Abel Brian , Newell Evan W , Bettinotti Maria P. , Benner Sarah E. , Patel Eshan U. , Littlefield Kirsten , Laeyendecker Oliver , Shoham Shmuel , Sullivan David , Casadevall Arturo , Pekosz Andrew , Nardin Alessandra , Fehlings Michael , Tobian Aaron AR , Quinn Thomas C 
Published: October 2020

AbstractCharacterization of the T cell response in individuals who recover from SARS-CoV-2 infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 COVID-19 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis, humoral and inflammatory responses. 132 distinct SARS-CoV-2-specific CD8+ T cell epitope responses across six different HLAs were detected, corresponding to 52 unique reactivities. T cell responses were directed against several structural and non-structural virus proteins. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem-cell and transitional memory states, subsets, which may be key to developing durable protection.
The impact of preprint servers in the formation of novel ideas
Authors: Satish Swarup , Yao Zonghai , Drozdov Andrew , Veytsman Boris 
Published: October 2020

AbstractWe study whether novel ideas in biomedical literature appear first in preprints or traditional journals. We develop a Bayesian method to estimate the time of appearance for a phrase in the literature, and apply it to a number of phrases, both automatically extracted and suggested by experts. We see that presently most phrases appear first in the traditional journals, but there is a number of phrases with the first appearance on preprint servers. A comparison of the general composition of texts from bioRxiv and traditional journals shows a growing trend of bioRxiv being predictive of traditional journals. We discuss the application of the method for related problems.
Synergistic effect of deoxynucleosides and AAV gene therapy for thymidine kinase 2 deficiency
Authors: Lopez-Gomez Carlos , Sanchez-Quintero Maria J. , Lee Eung Jeon , Kleiner Gulio , Xie Jun , Akman Hasan Orhan , Gao Guangping , Hirano Michio 
Published: October 2020

AbstractAutosomal recessive thymidine kinase 2 (TK2) mutations causes TK2 deficiency, which typically manifests as a progressive and fatal mitochondrial myopathy in infants and children. Treatment with deoxycytidine and thymidine ameliorates mitochondrial defects and extends lifespan ofTk2knock-in mouse (TK2−/−); however, efficacy is limited by age- and tissue-dependent expression of the cytosolic enzymes Tk1 and Dck. Thus, therapies aimed at systemic restoration of TK2 activity are needed. Here, we demonstrate that delivery of human TK2 cDNA to Tk2−/−mice using AAV9 efficiently rescued Tk2 activity in all the tissues tested except kidney, delayed disease onset, and increased lifespan. Sequential treatment of Tk2−/−mice with AAV9 first followed by AAV2 at different ages allowed us to reduce the viral dose while further prolonging the lifespan. Furthermore, addition of deoxycytidine and deoxythymidine supplementation to AAV9 + AAV2 treated Tk2−/−mice dramatically improved mtDNA copy numbers in liver and kidney, animal growth, and lifespan. These data indicate that combined pharmacological and gene therapies may be highly efficacious for human TK2 deficiency.
Joint automatic metabolite identification and quantification of a set of1H NMR spectra
Authors: Lefort Gaëlle , Liaubet Laurence , Marty-Gasset Nathalie , Canlet Cécile , Vialaneix Nathalie , Servien Rémi 
Published: October 2020

AbstractMetabolomics is a promising approach to characterize phenotypes or to identify biomarkers. It is also easily accessible through NMR, which can provide a comprehensive understanding of the metabolome of any living organisms. However, the analysis of1H NMR spectrum remains difficult, mainly due to the different problems encountered to perform automatic identification and quantification of metabolites in a reproducible way. In addition, methods that perform automatic identification and quantification of metabolites often do it for one given complex mixture spectrum. Hence, when a set of complex mixture spectra coming from the same experiment has to be processed, the approach is simply repeated independently for every spectrum, despite their resemblance. Here, we present a new method that is the first to identify and quantify metabolites by integrating information coming from several complex spectra of the same experiment. The performances of this new method are then evaluated on both simulated and real datasets. The results show an improvement in the metabolite identification and in the accuracy of metabolite quantifications, especially when the concentration is low. This joint procedure is available in version 2.0 ofASICSpackage.
Angiotensin-converting enzyme 2 (ACE2) is upregulated in Alzheimer’s disease brain
Authors: Ding Qiyue , Shults Nataliia V. , Harris Brent T. , Suzuki Yuichiro J. 
Published: October 2020

AbstractAlzheimer’s disease is a chronic neurodegenerative disorder and represents the main cause of dementia. Currently, the world is suffering from the pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses angiotensin-converting enzyme 2 (ACE2) as a receptor to enter the host cells. In COVID-19, neurological manifestations have been reported to occur. The present study demonstrates that the protein expression level of ACE2 is upregulated in the brain of Alzheimer’s disease patients. The increased ACE2 expression is not age-dependent, suggesting the direct relationship between Alzheimer’s disease and the ACE2 expression. Oxidative stress has been implicated in the pathogenesis of Alzheimer’s disease, and Alzheimer’s disease brains examined in this study also exhibited higher carbonylated proteins as well as increased thiol oxidation state of peroxiredoxin 6 (Prx6). The positive correlation was found between the increased ACE2 protein expression and oxidative stress in Alzheimer’s disease brain. Thus, the present study reveals the relationships between Alzheimer’s disease and ACE2, the receptor for SARS-CoV-2. These results warrant monitoring Alzheimer’s disease patients with COVID-19 carefully for the possible higher viral load in the brain and long-term adverse neurological consequences.
TheRpi-mcq1resistance gene family recognizesAvr2ofPhytophthora infestansbut is distinct fromR2
Authors: Aguilera-Galvez Carolina , Chu Zhaohui , Omy Sumaiya Haque , Wouters Doret , Gilroy Eleanor M. , Vossen Jack H. , Visser Richard G.F , Birch Paul , Jones Jonathan D.G , Vleeshouwers Vivianne G.A.A 
Published: October 2020

AbstractPotato late blight, which is caused by the destructive oomycete pathogenPhytophthora infestans, is a major threat to global food security. Several nucleotide binding, leucine-rich repeat (NLR)ResistancetoP. infestans(Rpi) genes have been introgressed into potato cultivars from wildSolanumspecies that are native to Mexico, but these were quickly defeated. Positional cloning inSolanum mochiquense, combined with allele mining inSolanum huancabambense,were used to identify a new family ofRpigenes from PeruvianSolanumspecies.Rpi-mcq1,Rpi-hcb1.1andRpi-hcb1.2confer race-specific resistance to a panel ofP. infestansisolates. Effector assays showed that theRpi-mcq1family mediates a hypersensitive response upon recognition of the RXLR effector AVR2, which had previously been found to be exclusively recognized by the family of R2 resistance proteins. TheRpi-mcq1andR2genes are distinct and reside on chromosome IX and IV, respectively. This is the first report of two unrelated R protein families that recognize the same AVR protein. We anticipate that this likely is a consequence of a geographically separated dynamic co-evolution ofRgene families ofSolanumwith an important effector gene ofP. infestans.Author summaryPotato is the largest non-grain staple crop and essential for food security world-wide. However, potato plants are continuously threatened by the notorious oomycete pathogenPhytophthora infestansthat causes late blight. This devastating disease has led to the Irish famine more then 150 years ago, and is still a major threat for potato. Resistance againstP. infestanscan be found in wild relatives of potato, which carry resistance genes that belong to the nucleotide binding site-leucine-rich repeat (NLR) class. Known NLR proteins typically recognize a matching effector fromPhytophthora, which leads to a hypersensitive resistance response (HR). For example, R2 from MexicanSolanumspecies recognizes AVR2 fromP. infestans. So far, theseRgenes exclusively match to oneAvrgene. Here, we identified a new class of NLR proteins that are different from R2, but also recognize the same effector AVR2. This new family of NLR occurs in South AmericanSolanumspecies, and we anticipate that it is likely a product of a geographically separated co-evolution with AVR2. This is the first report of two unrelated R protein families that recognize the same AVR protein.
The Bioprocess TEA Calculator: An online techno-economic analysis tool to evaluate the commercial competitiveness of potential bioprocesses
Authors: Lynch Michael D. 
Published: October 2020

AbstractTechno-economic analysis connects R&D, engineering, and business. By linking process parameters to financial metrics, it allows researchers to understand the factors controlling the potential success of their technologies. In particular, metabolic and bioprocess engineering, as disciplines, are aimed at engineering cells to synthesize products with an ultimate goal of commercial deployment. As a result it is critical to be able to understand the potential impact of strain engineering strategies and lab scale results on commercial potential. To date, while numerous techno-economic models have been developed for a wide variety of bioprocesses, they have either required process engineering expertise to adapt and/or use or do not directly connect financial outcomes to potential strain engineering results. Despite the clear value of techno-economic analysis, these challenges have made it inaccessible to many researchers. I have developed this online calculator (https://bioprocesstea.comORhttp://bioprocess-tea-calculator.herokuapp.com/) to make the basic capabilities of early-stage techno-economic analysis of bioprocesses readily accessible. The tool, currently focused on aerobic fermentation processes, can be used to understand the impact of fermentation level metrics on the commercial potential of a bioprocess for the production of a wide variety of organic molecules. Using the calculator, I review the commercially relevant targets for an aerobic bioprocess for the production of diethyl malonate.HighlightsA generalized techno-economic analysis tool for aerobic fermentation based bioprocesses.Relates strain and process improvements to projected commercial financial outcomesCommercial bioprocess targets to produce diethyl malonate are estimated to include fermentation titers >150 g/L, rates > 5g/L-hr and > 90% yield, with downstream purification yields > 90% and purification costs limited to less than 20% of total.
Metal Dependent Dynamic Equilibrium: A Regulatory Mechanism for M17 Aminopeptidases fromPlasmodium falciparumandPlasmodium vivax
Authors: Malcolm Tess R. , Belousoff Matthew J. , Venugopal Hariprasad , Borg Natalie A. , Drinkwater Nyssa , Atkinson Sarah C. , McGowan Sheena 
Published: October 2020

AbstractM17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases fromPlasmodium falciparum(PfA-M17) andPlasmodium vivax(Pv-M17) function as catalytically active hexamers to acquire free amino acids from human hemoglobin and are drug targets for the design of novel anti-malarial agents. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found thatPfA-M17 andPv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species, that can be controlled by manipulating the identity and concentration of metal ions available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of thePv-M17 hexameric species revealed thatPfA-M17 andPv-M17 bind metal ions and substrates in a conserved fashion, althoughPv-M17 forms the active hexamer more readily and processes substrates faster thanPfA-M17. On the basis of solution studies and structures determined by cryo-electron microscopy, we propose a dynamic equilibrium between monomer dimer tetramer hexamer, which becomes directional towards the large oligomeric states with the addition of metal ions. M17 aminopeptidases can exploit this sophisticated metal-dependent dynamic equilibrium to regulate formation of the catalytically active hexamer and therefore regulate catalysis.
Implantation and Gastrulation Abnormalities Characterize Early Embryonic Lethal Mouse Lines
Authors: Yoon Yeonsoo , Riley Joy , Gallant Judith , Xu Ping , Rivera-Pérez Jaime A. 
Published: October 2020

SummaryThe period of development between the zygote and embryonic day 9.5 in mice includes multiple developmental milestones essential for embryogenesis. The preeminence of this period of development has been illustrated in loss of function studies conducted by the International Mouse Phenotyping Consortium (IMPC) which have shown that close to one third of all mouse genes are essential for survival to weaning age and a significant number of mutations cause embryo lethality before E9.5. Here we report a systematic analysis of 21 pre-E9.5 lethal lines generated by the IMPC. Analysis of pre- and post-implantation embryos revealed that the majority of the lines exhibit mutant phenotypes that fall within a window of development between implantation and gastrulation with few pre-implantation and no post-gastrulation phenotypes. Our study provides multiple genetic inroads into the molecular mechanisms that control early mammalian development and the etiology of human disease, in particular, the genetic bases of infertility and pregnancy loss. We propose a strategy for an efficient assessment of early embryonic lethal mutations that can be used to assign phenotypes to developmental milestones and outline the time of lethality.
Repeatability of soma and neurite metrics in cortical and subcortical grey matter
Authors: Genc Sila , Chamberland Maxime , Koller Kristin , Tax Chantal M.W. , Zhang Hui , Palombo Marco , Jones Derek K. 
Published: October 2020

AbstractDiffusion magnetic resonance imaging is a technique which has long been used to study white matter microstructurein vivo. Recent advancements in hardware and modelling techniques have opened up interest in disentangling tissue compartments in the grey matter. In this study, we evaluate the repeatability of soma and neurite density imaging in a sample of six healthy adults scanned five times on an ultra-strong gradient magnetic resonance scanner (300 mT/m). Repeatability was expressed as an intraclass correlation coefficient (ICC). Our findings reveal that measures of soma density (mean ICC=.976), neurite density (mean ICC=.959) and apparent soma size (mean ICC=.923) are highly reliable across multiple cortical and subcortical networks. Overall, we demonstrate the promise of moving advanced grey matter microstructural imaging towards applications of development, ageing, and disease.
Electrostatic Plasma Membrane Targeting Contributes to Dlg Function in Cell Polarity and Tumorigenesis
Authors: Lu Juan , Dong Wei , Tao Yan , Hong Yang 
Published: October 2020

SUMMARYDiscs large (Dlg) is an essential polarity protein and a tumor suppressor originally characterized inDrosophilabut is also well conserved in vertebrates. Like the majority of polarity proteins, plasma membrane (PM)/cortical localization of Dlg is required for its function in polarity and tumorigenesis, but the exact mechanisms targeting Dlg to PM remain to be fully elucidated. Here we show that, similar to the recently discovered polybasic polarity proteins such as Lgl and aPKC, Dlg also contains a positively charged polybasic domain that electrostatically binds the PM phosphoinositides PI4P and PI(4,5)P2. Electrostatic targeting by the polybasic domain contributes significantly to the PM localization of Dlg in follicular and early embryonic epithelial cells, and is crucial for Dlg to regulate both polarity and tumorigenesis. The electrostatic PM targeting of Dlg is controlled by a potential phosphorylation-dependent allosteric regulation of its polybasic domain, and is specifically enhanced by the interactions between Dlg and another basolateral polarity protein and tumor suppressor Scrib. Our studies highlight an increasingly significant role of electrostatic PM targeting of polarity proteins in regulating cell polarity.