bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression and functional evaluation of recombinant human ABO blood group antigen cleaving glycoside hydrolases α-N-acetylgalactosaminidase, α-galactosidase, and endo-β-galactosidase produced in Escherichia coli
Authors: Toh Wu Han , Kuo Yvonne , Hsu Sean Kai , Chen Bernie , Lee Alan Justin , Liaw Easton , Lee Jane , Cheng Alexander , Hwa Laura , Hu Kaitlyn , Chien Sienna , Wong Christine , Chang Kristin , Hang Minna , Hong Sabrina , Su Ethan , Clapper Jude , Hsu Jonathan 
Published: May 2022

AbstractBlood transfusions are an integral component of healthcare; however, availability of viable blood is limited by patient-donor blood type specificity, which contributes to seasonal shortages as well as shortages worldwide, especially in developing countries, and during pandemics or natural disasters. Attempts to increase blood supply with commercial incentives have raised ethical concerns, and current proposed artificial blood substitutes are unable to fully replicate the function of native red blood cells (RBCs). In this study, we explore the potential strategy of alleviating blood shortages through enzymatic conversion of A, B, and AB blood types to blood type O. In theory, this process eliminates ABO patient-donor incompatibility, which increases the supply of universal donor blood. Three glycoside hydrolases, α-N-acetylgalactosaminidase, α-galactosidase, and endo-β-galactosidase, were selected to act as molecular scissors to cleave terminal residues on A and B RBC surface antigens and catalyze the conversion process. These enzymes were recombinantly expressed in BL21(DE3) Escherichia coli and purified through nickel ion affinity chromatography. A combination of colorimetric substrate assays, thin-layer chromatography, and mass spectroscopy were utilized to evaluate enzyme functionality. Enzyme efficiency was modeled using Michaelis–Menten kinetics. Partial enzymatic A-to-O blood type conversion on porcine red blood cells was observed with slide agglutination tests. Results confirm recombinant enzyme-mediated blood type conversion as a potential strategy for alleviating blood shortages.
A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast
Authors: Grigaitis Pranas , Grundel Douwe A. J. , van Pelt-Kleinjan Eunice , Isaku Mirushe , Xie Guixiang , Farias Sebastian Mendoza , Teusink Bas , van Heerden Johan H. 
Published: May 2022

AbstractThe fission yeast Schizosaccharomyces pombe is a popular eukaryal model organism for cell division and cell cycle studies. With this extensive knowledge of its cell and molecular biology, S. pombe also holds promise for use in metabolism research and industrial applications. However, unlike the baker’s yeast Saccharomyces cerevisiae, a major workhorse in these areas, cell physiology and metabolism of S. pombe remain less explored. One way to advance understanding of organism-specific metabolism is construction of computational models and their use for hypothesis testing. To this end, we leverage existing knowledge of S. cerevisiae to generate a manually-curated high-quality reconstruction of S. pombe’s metabolic network, including a proteome-constrained version of the model. Using these models, we gain insights into the energy demands for growth, as well as ribosome kinetics in S. pombe. Furthermore, we predict proteome composition and identify growth-limiting constraints that determine optimal metabolic strategies under different glucose availability regimes, and reproduce experimentally determined metabolic profiles. Notably, we find similarities in metabolic and proteome predictions of S. pombe with S. cerevisiae, which indicate that similar cellular resource constraints operate to dictate metabolic organization. With these use cases, we show, on the one hand, how these models provide an efficient means to transfer metabolic knowledge from a well-studied to a lesser-studied organism, and on the other, how they can successfully be used to explore the metabolic behaviour and the role of resource allocation in driving different strategies in fission yeast.
Functional brain region-specific neural spheroids for modeling neurological diseases and therapeutics screening
Authors: Strong Caroline E. , Kundu Srikanya , Boutin Molly , Chen Yu-Chi , Wilson Kelli , Lee Emily , Ferrer Marc 
Published: May 2022

SUMMARY3D spheroids have emerged as powerful drug discovery tools given their high-throughput screening (HTS) compatibility. Here, we established a method for generating functional neural spheroids with differentiated human induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes at cell type compositions mimicking specific regions of the human brain. Recordings of intracellular calcium oscillations were used as functional assays, and the utility of this spheroids system was shown through disease modelling, drug testing, and formation of assembloids to model neurocircuitry. We developed disease models for Alzheimer’s and Parkinson’s Disease through incorporating genetically engineered cells into spheroids, and Opioid Use Disorder by chronically treating spheroids with DAMGO. We reversed baseline functional deficits in each disease model with clinically approved treatments and showed that assembloid activity can be chemogenetically manipulated. Here, we lay the groundwork for brain region-specific spheroids as a robust functional assay platform for HTS studies.
Ribotoxic collisions on CAG expansions disrupt proteostasis and stress responses in Huntington’s Disease
Authors: Aviner Ranen , Lee Ting-Ting , Masto Vincent B. , Gestaut Dan , Li Kathy H. , Andino Raul , Frydman Judith 
Published: May 2022

SummaryHuntington’s disease (HD) is a devastating neurodegenerative disorder caused by CAG trinucleotide repeat expansions encoding a polyglutamine (polyQ) tract in the Huntingtin (HTT) gene1. Although mutant HTT (mHTT) protein tends to aggregate, the exact causes of neurotoxicity in HD remain unclear2. Here we show that altered elongation kinetics on CAG expansions cause ribosome collisions that trigger ribotoxicity, proteotoxicity and maladaptive stress responses. CAG expansions cause an elongation rate conflict during HTT translation, when ribosomes rapidly decoding the optimal polyQ encounter a flanking slowly-decoded polyproline tract. The ensuing ribosome collisions lead to premature termination and release of aggregation-prone mHTT fragments. Due to the presence of a stress-responsive upstream open reading frame (uORF), HTT translation and aggregation are limited under normal conditions but enhanced under stress, seeding a vicious cycle of dysfunction. mHTT further exacerbates ribotoxicity by progressively sequestering eIF5A, a key regulator of translation elongation, polyamine metabolism and stress responses. eIF5A depletion in HD cells leads to widespread ribosome pausing on eIF5A-dependent sites, impaired cotranslational proteostasis, disrupted polyamine metabolism and maladaptive stress responses. Importantly, drugs that reduce translation initiation attenuate ribosome collisions and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
Responses of Model Cortical Neurons to Temporal Interference Stimulation and Related Transcranial Alternating Current Stimulation Modalities
Authors: Wang Boshuo , Aberra Aman S. , Grill Warren M. , Peterchev Angel V. 
Published: May 2022

AbstractObjectiveTemporal interference stimulation (TIS) was proposed as a non-invasive, focal, and steerable deep brain stimulation method. However, the mechanisms underlying experimentally-observed suprathreshold TIS effects are unknown, and prior simulation studies had limitations in the representations of the TIS electric field (E-field) and cerebral neurons. We examined the E-field and neural response characteristics for TIS and related transcranial alternating current stimulation modalities.ApproachUsing the uniform-field approximation, we simulated a range of stimulation parameters in biophysically realistic model cortical neurons, including different orientations, frequencies, amplitude ratios, amplitude modulation, and phase difference of the E-fields, and obtained thresholds for both activation and conduction block.Main resultsFor two E-fields with similar amplitudes (representative of E-field distributions at the target region), TIS generated an amplitude-modulated total E-field. Due to the phase difference of the individual E-fields, the total TIS E-field vector also exhibited rotation where the orientations of the two E-fields were not aligned (generally also at the target region). TIS activation thresholds (75–230 V/m) were similar to those of high-frequency stimulation with or without modulation and/or rotation. For E-field dominated by the high-frequency carrier and with minimal amplitude modulation and/or rotation (typically outside the target region), TIS was less effective at activation and more effective at block. Unlike amplitude-modulated high-frequency stimulation, TIS generated conduction block with some orientations and amplitude ratios of individual E-field at very high amplitudes of the total E-field (>1700 V/m).SignificanceThe complex 3D properties of the TIS E-fields should be accounted for in computational and experimental studies. The mechanisms of suprathreshold cortical TIS appear to involve neural activity block and periodic activation or onset response, consistent with computational studies of peripheral axons. These phenomena occur at E-field strengths too high to be delivered tolerably through scalp electrodes and may inhibit endogenous activity in off-target regions, suggesting limited significance of suprathreshold TIS.
Identifying disease-associated circRNAs based on edge-weighted graph attention and heterogeneous graph neural network
Authors: Lu Chengqian , Zhang Lishen , Zeng Min , Lan Wei , Wang Jianxin 
Published: May 2022

AbstractMotivationCircular RNAs (circRNAs) with varied biological activities are implicated in pathogenic processes, according to new findings. They are regarded as promising biomarkers for the diagnosis and prognosis due to their structural features. Computational approaches, as opposed to traditional experiments, can identify the circRNA-disease connections at a lower cost. Multi-source pathogenesis data can help to reduce data sparsity and infer probable connections at the system level. The majority of available approaches create a homologous network using multi-source data, but they lose the data’s heterogeneity. Effective solutions that make use of the peculiarities of multi-source data are urgently needed.ResultsIn this paper, we propose a model (CDHGNN) based on edge-weighted graph attention and heterogeneous graph neural networks for discovering probable circRNA-disease correlations prediction. The circRNA network, miRNA network, disease network and heterogeneous network are constructed based on the introduced multi-source data on circRNAs, miRNAs, and diseases. The features for each type of node in the network are then extracted using a designed edge-weighted graph attention network model. Using the revised node features, we learn meta-path contextual information and use heterogeneous neural networks to assign attention weights to different types of edges. CDHGNN outperforms state-of-the-art algorithms with comparable accuracy, according to the findings of the trial. Edge-weighted graph attention networks and heterogeneous graph networks have both improved performance significantly. Furthermore, case studies suggest that CDHGNN is capable of identifying particular molecular connections and can be used to investigate pathogenic pathways.Contactjxwang@mail.csu.edu.cn
Modelling the spread and mitigation of an emerging vector-borne pathogen; citrus greening in the U.S.
Authors: Nguyen Viet-Anh , Bartels David W. , Gilligan Christopher A. 
Published: May 2022

AbstractPredictive models, based upon epidemiological principles and fitted to surveillance data, play an increasingly important role in shaping regulatory and operational policies for emerging outbreaks. Data for parameterising these strategically important models are often scarce when rapid actions are required to change the course of an epidemic invading a new region. We provide a flexible toolkit for landscape-scale disease management, which is applicable to a range of emerging pathogens including vector-borne pathogens for both endemic and invading epidemic vectors. We use the toolkit to analyse and predict the spread of Huanglongbing disease or citrus greening in the U.S. We estimate epidemiological parameters using survey data from one region (Texas) and show how to transfer and test parameters to construct predictive spatio-temporal models for another region (California). The models are used to screen effective coordinated and reactive management strategies for different regions.
Identification of neoantigens in esophageal adenocarcinoma
Authors: Nicholas Ben , Bailey Alistair , McCann Katy J , Wood Oliver , Walker Robert C , Parker Robert , Ternette Nicola , Elliott Tim , Underwood Tim J , Johnson Peter , Skipp Paul 
Published: May 2022

AbstractEsophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for immunotherapy are short peptide neoantigens containing tumor mutations, presented to cytotoxic T-cells by human leukocyte antigen molecules (HLA). Despite an association between putative neoantigen abundance and therapeutic response across cancers, immunogenic neoantigens are challenging to identify. Here we characterized the mutational and immunopeptidomic landscapes of tumors from a cohort of seven patients with EAC. We directly identified one HLA-I presented neoantigen from one patient, and report functional T-cell responses from a predicted HLA-II neoantigen in a second patient. The predicted class II neoantigen contains both HLA I and II binding motifs. Our exploratory observations are consistent with previous neoantigen studies in finding that neoantigens are rarely directly observed, and an identification success rate following prediction in the order of 10%. However, our identified putative neoantigen is capable of eliciting strong T-cell responses, emphasizing the need for improved strategies for neoantigen identification.
An autonomous mathematical model for the mammalian cell cycle
Authors: Williams Katherine S. , Secomb Timothy W. , El-Kareh Ardith W. 
Published: May 2022

AbstractA mathematical model for the mammalian cell cycle is developed as a system of 13 coupled nonlinear ordinary differential equations. The variables and interactions included in the model are based on detailed consideration of available experimental data. Key features are that the model is autonomous, except for dependence on external growth factors; variables are continuous in time, without instantaneous resets at phase boundaries; cell cycle controllers and completion of tasks associated with cell cycle progression are represented; mechanisms to prevent rereplication are included; and cycle progression is independent of cell size. Eight variables represent cell cycle controllers: Cyclin D1 in complex with Cdk4/6, APCCdh1, SCFβTrcp, Cdc25A, MPF, NUMA, securin-separase complex, and separase. Five variables represent task completion, with four for the status of origins and one for kinetochore attachment. The model predicts distinct behaviors consistent with each main phase of the cell cycle. The response to growth factors shows restriction-point behavior. These results imply that the main features of the mammalian cell cycle can be accounted for in a quantitative mechanistic way based on known interactions among cycle control factors and their coupling to tasks involved in replication of DNA. The model is robust to parameter changes, in that cycling is maintained over at least a five-fold range of each parameter when varied individually. The most sensitive parameters are those associated with the initiation and completion of mitosis. The model is suitable for exploring how extracellular factors affect cell cycle progression, including responses to metabolic conditions and to anti-cancer therapies.Author SummaryWe created a model, that is, a set of mathematical equations, to represent the entire cell cycle in mammals. All terms in our equations correspond to actual biological mechanisms. We solved the equations and verified that they show similar behavior to real-life cell cycles. We designed our model to cycle only when enough external growth factors stimulate it, as real cells do. Our model helps us better understand how the cell cycle is controlled. One very important aspect of control is how the cell ensures that its DNA is copied only once per cell cycle. If “rereplication” (copying a section of DNA twice in the same cycle) occurs, it can cause harmful DNA damage. We considered several mechanisms that some biologists believe play a role, and found that most could not explain how rare rereplication is. Two mechanisms did work well, and we used them to make two variants of the model, which show similar behavior. The model has many potential applications. The cell cycle is altered in most cancer cells, so understanding how these changes affect control is useful. Many widely-used drugs affect the cell cycle, and our model can be used to study these effects.
Development of a Well-Characterized Cynomolgus Macaque Model of Sudan Virus Disease for Support of Product Development
Authors: Alfson Kendra J. , Goez-Gazi Yenny , Gazi Michal , Chou Ying-Liang , Niemuth Nancy A. , Mattix Marc E. , Staples Hilary , Klaffke Benjamin , Rodriguez Gloria F. , Escareno Priscilla , Bartley Carmen , Ticer Anysha , Clemmons Elizabeth A. , Dutton John W. , Griffiths Anthony , Meister Gabe T. , Sanford Daniel C. , Cirimotich Chris M. , Carrion Ricardo 
Published: May 2022

AbstractThe primary objective of this study was to characterize the disease course in cynomolgus macaques exposed to Sudan virus (SUDV), to determine if infection in this species is an appropriate model for the evaluation of filovirus countermeasures under the FDA Animal Rule. Sudan virus causes Sudan virus disease (SVD), with an average case fatality rate of approximately 50%, and while research is ongoing, presently there are no approved SUDV vaccines or therapies. Well characterized animal models are crucial for further developing and evaluating countermeasures for SUDV. Twenty (20) cynomolgus macaques were exposed intramuscularly to either SUDV or sterile phosphate buffered saline; 10 SUDV-exposed animals were euthanized on schedule to characterize pathology at defined durations post-exposure and 8 SUDV-exposed animals were not part of the scheduled euthanasia cohort. Survival was assessed, along with clinical observations, body weights, body temperatures, hematology, clinical chemistry, coagulation, viral load (serum and tissues), macroscopic observations, and histopathology. There were statistically significant differences between SUDV-exposed animals and mock-exposed animals for 26 parameters, including telemetry body temperature, clinical chemistry parameters, hematology parameters, activated partial thromboplastin time, serum viremia, and biomarkers that characterize the disease course of SUDV in cynomolgus macaques.
Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA
Authors: Stone Sharon Emily , Ray Dhiman , Andricioaei Ioan 
Published: May 2022

AbstractThe Hoogsteen (HG) base pairing (bp) conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and non-bonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.Graphical TOC Entry
Three-dimensional envelope and subunit interactions of the plastid-encoded RNA polymerase from Sinapis alba
Authors: Ruedas Rémi , Couté Yohann , Kieffer-Jacquinod Sylvie , Sankari Muthukumar Soumiya , Gillet François-Xavier , Fenel Daphna , Effantin Grégory , Pfannschmidt Thomas , Blanvillain Robert , Cobessi David 
Published: May 2022

AbstractRNA polymerases (RNAPs) involved in gene transcription are found in all living organisms with degrees of complexity ranging from single polypeptide chains to multimeric enzymes. In the chloroplasts, the nuclear-encoded RNA polymerase and the plastid-encoded RNA polymerase (PEP) are both involved in the selective transcription of the plastid genome. The PEP is a prokaryotic-type multimeric RNAP found in different states depending on light stimuli and cell identity. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa regarded as essential for chloroplast biogenesis. A purification procedure compatible with structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. Mass spectrometry (MS)-based proteomic analysis identified the core components, the PAPs and additional members, and coupled to cross-linking (XL-MS) provided initial structural information about the relative position of PEP subunits. Sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that the overall shape of the catalytic core and the residues essential for the catalytic activity are conserved. However, variations are observed at the surface of the core, some of them corresponding to PAP binding sites as suggested by XL-MS experiments. Using negative stain electron microscopy, the PEP 3D envelope was calculated. 3D classification shows that the protrusions which we attribute to the PAPs are firmly associated with the catalytic core. Overall, the shape of the S. alba PEP envelope is different from that of RNAPs.