bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling a co-culture ofClostridium autoethanogenumandClostridium kluyverito increase syngas conversion to medium-chain fatty-acids
Authors: Benito-Vaquerizo Sara , Diender Martijn , Olm Ivette Parera , dos Santos Vitor Martins , Schaap Peter J. , Sousa Diana Z. , Suarez-Diez Maria 
Published: June 2020

AbstractMicrobial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use ofClostridiumspecies for the production of small organic molecules such as ethanol and acetate. The cocultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture ofClostridium autoethanogenumandClostridium kluyverion syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that addition of succinate is one strategy to optimize the production of medium-chain fatty-acids from syngas with this co-culture. According to the predictions, addition of succinate increases the pool of crotonyl-CoA and the ethanol/acetate uptake ratio inC. kluyveri, resulting in the flux of up to 60% of electrons into hexanoate. Other potential way to optimize butyrate and hexanoate is to increase ethanol production byC. autoethanogenum. Deletion of either formate transport, acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) from the metabolic model ofC. autoethanogenumleads to a (potential) increase in ethanol production up to 150%, which is clearly very attractive.
A predictive model of gene expression reveals the role of regulatory motifs in the mating response of yeast
Authors: Pomeroy Amy E. , Pena Matthew I. , Houser John R. , Dixit Gauri , Dohlman Henrik G. , Elston Timothy C. , Errede Beverly 
Published: June 2020

ABSTRACTCells use signaling pathways to receive and process information about their environment. These systems are nonlinear, relying on feedback and feedforward regulation to respond appropriately to changing environmental conditions. Mathematical models developed to describe signaling pathways often fail to show predictive power, because the models are not trained on data that probe the diverse time scales on which feedforward and feedback regulation operate. We addressed this limitation using microfluidics to expose cells to a broad range of dynamic environmental conditions. In particular, we focus on the well-characterized mating response pathway ofS. cerevisiae(yeast). This pathway is activated by mating pheromone and initiates the transcriptional changes required for mating. Although much is known about the molecular components of the mating response pathway, less is known about how these components function as a dynamical system. Our experimental data revealed that pheromone-induced transcription persists following removal of pheromone and that long-term adaptation of the transcriptional response occurs when pheromone exposure is sustained. We developed a model of the regulatory network that captured both persistence and long-term adaptation of the mating response. We fit this model to experimental data using an evolutionary algorithm and used the parameterized model to predict scenarios for which it was not trained, including different temporal stimulus profiles and genetic perturbations to pathway components. Our model allowed us to establish the role of four regulatory motifs in coordinating pathway response to persistent and dynamic stimulation.
Trypanocidal activity of the anthocyanidin delphinidin, a non-competitive inhibitor of arginine kinase
Authors: Valera-Vera Edward , Reigada Chantal , Sayé Melisa , Digirolamo Fabio A. , Galceran Facundo , Miranda Mariana R. , Pereira Claudio A. 
Published: June 2020

ABSTRACTThe enzyme arginine kinase fromTrypanosoma cruzi(TcAK) catalyzes the interconversion of arginine and phosphoarginine to maintain the ATP/ADP cell balance, and is involved in the parasites energetic homeostasis and stress responses. Using virtual screening approaches, some plant-derived polyphenolic pigments such as anthocyanidins, were predicted to inhibit TcAK activity. In this work, it was demonstrated that the anthocyanidin delphinidin showed a non-competitive inhibition mechanism of TcAKin vitro(Ki arginine = 1.32 μM and Ki ATP = 500 μM). Molecular docking simulations predicted that delphinidin occupies a hydrophobic pocket close to the ATP/ADP binding site. Delphinidin also exerted trypanocidal activity overT. cruzitrypomastigotes with a calculated IC50of 19.51 μM. Anthocyanidins are low-toxicity natural products which can be exploited for the development of trypanocidal drugs with less secondary effects than those currently used for the treatment of Chagas disease.
Cogno-Vest: A Torso-Worn, Force Display to Experimentally Induce Specific Hallucinations and Related Bodily Sensations
Authors: Fadaei J. Atena , Jeanmonod Kenny , Kannape Olivier A. , Potheegadoo Jevita , Bleuler Hannes , Hara Masayuki , Blanke Olaf 
Published: June 2020

AbstractRecent advances in virtual reality and robotic technologies have allowed researchers to explore the mechanisms underlying bodily aspects of self-consciousness which are largely attributed to the multisensory and sensorimotor processing of bodily signals (bodily self-consciousness, BSC). One key contribution to BSC, that is currently poorly addressed due to the lack of a wearable solution, concerns realistic collision sensations on the torso. Here, we introduce and validate a novel torso-worn force display, the Cogno-vest, to provide mechanical touch on the user’s back in a sensorimotor perception experiment. In a first empirical study, we characterized human finger poking (N=28). In order to match these poking characteristics and meet the wearability criteria, we used bi-directional, push-pull solenoids as a force actuator in the Cogno-vest. Subsequently, and based on an iterative, multidisciplinary design procedure, a bodyconforming, unisex, torso-worn force display was prototyped. Finally, we conducted a behavioral study that investigated BSC in 25 healthy participants by introducing conflicting sensorimotor signals between their hand and torso (back). Using the final reiteration of the Cogno-vest we successfully replicated previous findings on illusory states of BSC, characterized by presence hallucinations (PH) and passivity symptoms, and achieved higher illusion ratings compared to static conditions used in prior studies.
Drosophila Hedgehog can act as a morphogen in the absence of regulated Ci processing
Authors: Little Jamie C. , Garcia-Garcia Elisa , Sul Amanda , Kalderon Daniel 
Published: June 2020

SummaryExtracellular Hedgehog (Hh) proteins induce transcriptional changes in target cells by inhibiting the proteolytic processing of full-length Drosophila Ci or mammalian Gli proteins to nuclear transcriptional repressors and by activating the full-length proteins, which are otherwise held inactive by cytoplasmic binding partners and subject to accelerated degradation following activation. We used Ci variants expressed at physiological levels to investigate the contributions of these mechanisms to dose-dependent Hh signaling at the anteroposterior (AP) border of Drosophila wing imaginal discs. Ci variants that cannot be processed supported a normal pattern of graded target gene activation and the development of adults with normal wing morphology when supplemented by constitutive Ci repressor, showing that Hh can signal normally in the absence of regulated processing. The full-length Ci-155 protein profile of these variants revealed a linear gradient of Hh-stimulated degradation, allowing derivation of a spatial profile of inhibition of processing of normal C-155 by Hh. The processing-resistant Ci variants were also significantly activated in the absence of Hh by elimination of Cos2, acting through association with the CORD domain of Ci, or PKA, revealing separate inhibitory roles of these two components in addition to their well-established roles in promoting Ci-155 processing.
Transcriptomic and proteomic regulation through abundant, dynamic, and independent arginine methylation by Type I and Type II PRMTs
Authors: Lehman Stephanie M. , Chen Hongshan , Burgos Emmanuel S. , Maron Maxim , Gayatri Sitaram , Nieves Edward , Bai Dina L. , Sidoli Simone , Gupta Varun , Marunde Matthew R. , Bone James R. , Sun Zu-Wen , Bedford Mark T. , Shabanowitz Jeffrey , Hunt Donald F. , Shechter David 
Published: June 2020

AbstractArginine methylation is essential for both cellular viability and development and is also dysregulated in cancer. PRMTs catalyze the post translational monomethylation (Rme1/MMA, catalyzed by Type I-III), asymmetric (Rme2a/ADMA, Type I enzymes)-, or symmetric (Rme2s/SDMA, Type II enzymes) dimethylation of arginine. Despite many studies, a thorough integration of PRMT enzyme substrate determination and proteomic and transcriptomic consequences of inhibiting Type I and II PRMTs is lacking. To characterize cellular substrates for Type I (Rme2a) and Type II (Rme2s) PRMTs, human A549 lung adenocarcinoma cells were treated with either Type I (MS023) or Type II (GSK591) inhibitors. Using total proteome hydrolysis, we developed a new mass spectrometry approach to analyze total arginine and lysine content. We showed that Rme1 was a minor population (∼0.1% of total arginine), Rme2a was highly abundant (∼1.1%), and Rme2s was intermediate (∼0.4%). While Rme2s was mostly eliminated by GSK591 treatment, total Rme1 and Rme2a were more resistant to perturbation. To quantitatively characterize substrate preferences of the major enzymes PRMT1, PRMT4(CARM1), and PRMT5, we used oriented peptide array libraries (OPAL) in methyltransferase assays. We demonstrated that while PRMT5 tolerates aspartic acid residues in the substrate, PRMT1 does not. Importantly, PRMT4 methylated previously uncharacterized hydrophobic motifs. To integrate our studies, we performed PTMScan on PRMT-inhibited A549 cells and enriched for methylated arginine containing tryptic peptides. For detection of highly charged peptides, a method to analyze the samples using electron transfer dissociation was developed. Proteomic analysis revealed distinct methylated species enriched in nuclear function, RNA-binding, intrinsically disordered domains, and liquid-liquid phase separation. Parallel studies with proteomics and RNA-Seq revealed distinct, but ontologically overlapping, consequences to PRMT inhibition. Overall, we demonstrate a wider PRMT substrate diversity and methylarginine functional consequence than previously shown.
Elevated somatic mutation burdens in normal human cells due to defective DNA polymerases
Authors: Robinson Philip S. , Coorens Tim H.H. , Palles Claire , Mitchell Emily , Abascal Federico , Olafsson Sigurgeir , Lee Bernard , Lawson Andrew R.J. , Lee-Six Henry , Moore Luiza , Sanders Mathijs A. , Hewinson James , Martin Lynn , Pinna Claudia M.A. , Galvotti Sara , Campbell Peter J. , Martincorena Iñigo , Tomlinson Ian , Stratton Michael R. 
Published: June 2020

ABSTRACTMutation accumulation over time in normal somatic cells contributes to cancer development and is proposed as a cause of ageing. DNA polymerases Pol ε and Pol δ replicate DNA with high fidelity during normal cell divisions. However, in some cancers defective proofreading due to acquired mutations in the exonuclease domains of POLE or POLD1 causes markedly elevated somatic mutation burdens with distinctive mutational signatures. POLE and POLD1 exonuclease domain mutations also cause familial cancer predisposition when inherited through the germline. Here, we sequenced normal tissue DNA from individuals with germline POLE or POLD1 exonuclease domain mutations. Increased mutation burdens with characteristic mutational signatures were found to varying extents in all normal adult somatic cell types examined, during early embryogenesis and in sperm. Mutation burdens were further markedly elevated in neoplasms from these individuals. Thus human physiology is able to tolerate ubiquitously elevated mutation burdens. Indeed, with the exception of early onset cancer, individuals with germline POLE and POLD1 exonuclease domain mutations are not reported to show abnormal phenotypic features, including those of premature ageing. The results, therefore, do not support a simple model in which all features of ageing are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence by different hardwood tree species
Authors: Kelly Charlene N. , Schwaner Geoffrey W. , Cumming Jonathan R. , Driscoll Timothy P. 
Published: June 2020

AbstractThe soil microbiome plays an essential role in processing and storage of nitrogen (N) and carbon (C), and is influenced by vegetation above-ground through imparted differences in chemistry, structure, mass of plant litter, root physiology, and dominant mycorrhizal associations. We used shotgun metagenomic sequencing and bioinformatic analysis to quantify the abundance and distribution of gene families involved in soil microbial N and C cycling beneath three deciduous hardwood tree species: ectomycorrhizal (ECM)-associatedQuercus rubra(red oak), ECM-associatedCastanea dentata(American chestnut), and arbuscular mycorrhizal (AM)-associatedPrunus serotina(black cherry). Chestnut exhibited the most distinct soil microbiome of the three species, both functionally and taxonomically, with a general suppression of functional genes in the nitrification, denitrification, and nitrate reduction pathways. These changes were related to low inorganic N availability in chestnut stands as soil was modified by poor, low-N litter quality relative to red oak and black cherry soils.IMPORTANCEPrevious studies have used field biogeochemical process rates, isotopic tracing, and targeted gene abundance measurements to study the influence of tree species on ecosystem N and C dynamics. However, these approaches do not enable a comprehensive systems-level understanding of the relationship between microbial diversity and metabolism of N and C below-ground. We analyzed microbial metagenomes from soils beneath red oak, American chestnut, and black cherry stands and showed that tree species can mediate the abundance of key microbial genes involved in N and (to a lesser extent) C metabolism pathways in soil. Our results highlight the genetic framework underlying tree species’ control over soil microbial communities, and below-ground C and N metabolism, and may enable land managers to select tree species to maximize C and N storage in soils.
Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries
Authors: Kwong Alan M. , Blackwell Thomas W. , LeFaive Jonathon , de Andrade Mariza , Barnard John , Barnes Kathleen C. , Blangero John , Boerwinkle Eric , Burchard Esteban G. , Cade Brian E. , Chasman Daniel I. , Chen Han , Conomos Matthew P. , Cupples L. Adrienne , Ellinor Patrick T. , Eng Celeste , Gao Yan , Guo Xiuqing , Irvin Marguerite Ryan , Kelly Tanika N. , Kim Wonji , Kooperberg Charles , Lubitz Steven A. , Mak Angel C. Y. , Manichaikul Ani W. , Mathias Rasika A. , Montasser May E. , Montgomery Courtney G. , Musani Solomon , Palmer Nicholette D. , Peloso Gina M. , Qiao Dandi , Reiner Alexander P. , Roden Dan M. , Shoemaker M. Benjamin , Smith Jennifer A. , Smith Nicholas L. , Su Jessica Lasky , Tiwari Hemant K. , Weeks Daniel E. , Weiss Scott T. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,   TOPMed Analysis Working Group, Scott Laura J. , Smith Albert V. , Abecasis Gonçalo R. , Boehnke Michael , Kang Hyun Min 
Published: June 2020

ABSTRACTTraditional Hardy-Weinberg equilibrium (HWE) tests (the χ2test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in datasets comprised of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and evaluate the impact of population heterogeneity and genotype uncertainty on the standard HWE tests and alternative methods using simulated and real sequence datasets. Our results demonstrate that ignoring population structure or genotype uncertainty in HWE tests can inflate false positive rates by many orders of magnitude. Our evaluations demonstrate different tradeoffs between false positives and statistical power across the methods, with RUTH consistently amongst the best across all evaluations. RUTH is implemented as a practical and scalable software tool to rapidly perform HWE tests across millions of markers and hundreds of thousands of individuals while supporting standard VCF/BCF formats. RUTH is publicly available athttps://www.github.com/statgen/ruth.
Hypomyelination reduces parvalbumin interneuron density and auditory cortex inhibitory function
Authors: de Carvalho Borges Beatriz , Meng Xiangying , Long Patrick , Kanold Patrick Oliver , Corfas Gabriel 
Published: June 2020

ABSTRACTFor a long time, myelin was thought to be restricted to excitatory neurons, and studies on dysmyelination focused primarily on excitatory cells. Recent evidence showed that axons of inhibitory neurons in the neocortex are also myelinated, but the role of myelin on inhibitory circuits remains unknown. Here we studied the impact of mild hypomyelination on both excitatory and inhibitory connectivity in the primary auditory cortex (A1) with well-characterized mouse models of hypomyelination due to loss of oligodendrocyte ErbB receptor signaling. Using laser-scanning photostimulation, we found that mice with mild hypomyelination have reduced functional inhibitory connections to A1 L2/3 neurons without changes in excitatory connections, resulting in altered excitatory/inhibitory balance. These effects are not associated with altered expression of GABAergic and glutamatergic synaptic components, but with reduced density of parvalbumin-positive (PV+) neurons, which reflects reduced PV expression by interneurons rather than PV+neuronal loss. While immunostaining shows that hypomyelination occurs in both PV+and PV-axons, there is a strong correlation between MBP and PV expression suggesting that myelination influences PV expression. Together, the results demonstrate that mild hypomyelination impacts A1 neuronal networks, reducing inhibitory activity, and shifting networks towards excitation.
Transcriptome and metabolome analysis of crGART, a novel cell model of de novo purine synthesis deficiency: Alterations in CD36 expression and activity
Authors: Mazzarino Randall C , Baresova Veronika , Zikánová Marie , Duval Nathan , Wilkinson Terry G. , Patterson David , Vacano Guido N. 
Published: June 2020

ABSTRACTIn humans, GART [phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) / phosphoribosylglycinamide synthetase (EC 6.3.4.13) / phosphoribosylaminoimidazole synthetase (EC 6.3.3.1)] is a trifunctional protein which catalyzes the second, third, and fifth reactions of the ten step de novo purine synthesis (DNPS) pathway. The second step of DNPS is conversion of phosphoribosylamine (5-PRA) to glycineamide ribonucleotide (GAR). 5-PRA is extremely unstable under physiological conditions and is unlikely to accumulate in the absence of GART activity. Recently, a HeLa cell line null mutant for GART was constructed via CRISPR-Cas9 mutagenesis. This cell line, crGART, is an important cellular model of DNPS inactivation that does not accumulate DNPS pathway intermediates. In the current study, we characterized the crGART versus HeLa transcriptomes in purine-supplemented and purine-depleted growth conditions. We observed multiple transcriptome changes and discuss pathways and ontologies particularly relevant to Alzheimer disease and Down syndrome. We also report initial analysis of the Cluster of Differentiation (CD36) gene, which is highly expressed in crGART versus HeLa.
A novel and highly effective mitochondrial uncoupling drug in T-cell leukemia
Authors: da Silva-Diz Victoria , Cao Bin , Lancho Olga , Chiles Eric , Alasadi Amer , Luo Shirley , Augeri David , Minuzzo Sonia , Indraccolo Stefano , Su Xiaoyang , Jin Shengkan , Herranz Daniel 
Published: June 2020

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy. Despite recent advances in treatments with intensified chemotherapy regimens, relapse rates and associated morbidities remain high. In this context, metabolic dependencies have emerged as a druggable opportunity for the treatment of leukemia. Here, we tested the antileukemic effects of MB1-47, a newly developed mitochondrial uncoupling compound. MB1-47 treatment in T-ALL cells robustly inhibited cell proliferation via both cytostatic and cytotoxic effects as a result of compromised mitochondrial energy and macromolecule depletion, which severely impair nucleotide biosynthesis. Mechanistically, acute treatment with MB1-47 in primary leukemias promoted AMPK activation and downregulation of mTOR signaling, stalling anabolic pathways that support leukemic cell survival. Indeed, MB1-47 treatment in mice harboring murine NOTCH1-induced leukemias or human T-ALL PDXs led to a potent antileukemic effect with 2-fold extension in survival without overlapping toxicities. Overall, our findings demonstrate a critical role for mitochondrial oxidative phosphorylation in T-ALL and uncover MB1-47-driven mitochondrial uncoupling as a novel therapeutic strategy for the treatment of this disease.
Engineering a virus-like particle to display peptide insertions using an apparent fitness landscape
Authors: Robinson Stephanie A. , Hartman Emily C. , Ikwuagwu Bon C. , Francis Matthew B. , Tullman-Ercek Danielle 
Published: June 2020

ABSTRACTPeptide insertions in the primary sequence of proteins expand functionality by introducing new binding sequences, chemical handles, or membrane disrupting motifs. With these properties, proteins can be engineered as scaffolds for vaccines or targeted drug delivery vehicles. Virus-like particles (VLPs) are promising platforms for these applications since they are genetically simple, mimic viral structure for cell uptake, and can deliver multiple copies of a therapeutic agent to a given cell. Peptide insertions in the coat protein of VLPs can increase VLP uptake in cells by increasing cell binding, but it is difficult to predict how an insertion affects monomer folding and higher order assembly. To this end, we have engineered the MS2 VLP using a high-throughput technique, called Systematic Mutagenesis and Assembled Particle Selection (SyMAPS). In this work, we applied SyMAPS to investigate a highly mutable loop in the MS2 coat protein to display 9,261 non-native tripeptide insertions. This library generates a discrete map of three amino acid insertions permitted at this location, validates the FG loop as a valuable position for peptide insertion, and illuminates how properties such as charge, flexibility, and hydrogen bonding can interact to preserve or disrupt capsid assembly. Taken together, the results highlight the potential to engineer VLPs in systematic manner, paving the way to exploring the applications of peptide insertions in biomedically relevant settings.