bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of Soluble Expression of CTA1-(S14P5)4-DD and CTA1-(S21P2)4-DD Fusion Proteins as Candidates for COVID-19 Intranasal Vaccines
Authors: Tarigan Simson , Sumarningsih  , Sekarmila Gita , Apas  , Tarigan Ronald , Putri Ryandini , Setyawati Damai Ria 
Published: June 2024

AbstractDeveloping intranasal vaccines against pandemics and devastating airborne infectious diseases is imperative. The superiority of intranasal vaccines over injectable systemic vaccines is evident, but the challenge in developing effective intranasal vaccines is more substantial. Fusing a protein antigen with the catalytic domain of cholera toxin (CTA1) and the two-domain D of staphylococcal protein A (DD) has significant potential for intranasal vaccines. In the present study, we constructed two fusion proteins containing CTA1, tandem repeat linear epitopes of the SARS-CoV-2 spike protein (S14P5 or S21P2), and DD. Thein silicocharacteristics and solubility of the fusion proteins CTA1-(S14P5)4-DD and CTA1-(S21P2)4-DD were analyzed when overexpressed inEscherichia coli. Structural predictions indicated that each component of the fusion proteins was compatible with its origin. Both fusion proteins were predicted by computational tools to be soluble when overexpressed inE. coli. Contrary to these predictions, the constructs exhibited limited solubility. The solubility did not improve even after lowering the cultivation temperature from 37°C to 18°C. Induction with IPTG at the early log phase, instead of the usual mid-log phase growth, significantly increased soluble CTA1-(S21P2)4-DD but not CTA1-(S14P5)4-DD. The solubility of overexpressed fusion proteins significantly increased when a non-denaturing detergent (Nonidet P40, Triton X100, or Tween 20) was added to the extraction buffer. In a scale-up purification experiment, the yields were low, only 1-2 mg/L of culture, due to substantial losses during the purification stages, indicating the need for further optimization of the purification process.
Pseudomonastaxonomic and functional microdiversity in the wheat rhizosphere is cultivar- dependent and links to disease resistance profile and root diameter
Authors: Herms Courtney Horn , Hennessy Rosanna Catherine , Bak Frederik , Guan Ying , Browne Patrick Denis , Nielsen Tue Kjærgaard , Hansen Lars Hestbjerg , Dresbøll Dorte Bodin , Nicolaisen Mette Haubjerg 
Published: June 2024

AbstractDiversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to exploring intragenus microdiversity in an increasingly homogenous agricultural system. Through an integrative approach combining culture-dependent and -independent methods, we explore the rhizospherePseudomonaspangenome and demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related modern winter wheat cultivars. AFusarium-resistant cultivar demonstrated increasedPseudomonastaxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment ofPseudomonasisolates capable of antagonizingFusariumas well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely relatedPseudomonasisolates from the two cultures, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizospherePseudomonas.
Heterogeneity in establishment of polyethylene glycol-mediated plasmid transformations for five forest pathogenicPhytophthoraspecies
Authors: Dort Erika N. , Hamelin Richard C. 
Published: June 2024

AbstractPlasmid-mediated DNA transformation is a foundational molecular technique and the basis for most CRISPR-Cas9 gene editing systems. While plasmid transformations are well established for many agriculturalPhytophthorapathogens, development of this technique in forest Phytophthoras is lacking. Given our long-term research objective to develop CRISPR-Cas9 gene editing in a forest pathogenicPhytophthoraspecies, we sought to establish the functionality of polyethylene glycol (PEG)-mediated plasmid transformation in five species:P. cactorum,P. cinnamomi,P. cryptogea,P. ramorum, andP. syringae. We used the agricultural pathogenP. sojae, a species for which PEG-mediated transformations are well-established, as a transformation control. Using a protocol previously optimized forP. sojae, we tested transformations in the five forest Phytophthoras with three different plasmids: two developed for CRISPR-Cas9 gene editing and one developed for fluorescent protein tagging. Out of the five species tested, successful transformation, as indicated by stable growth of transformants on a high concentration of antibiotic selective growth medium and diagnostic PCR, was achieved only withP. cactorumandP. ramorum. However, while transformations inP. cactorumwere consistent and stable, transformations inP. ramorumwere highly variable and yielded transformants with very weak mycelial growth and abnormal morphology. Our results indicate thatP. cactorumis the best candidate to move forward with CRISPR-Cas9 protocol development and provide insight for future optimization of plasmid transformations in forest Phytophthoras.
An analysis of international strategies for monitoring and preventability described in medicinal product information: a study protocol
Authors: Sartori Daniele , Aronson Jeffrey K. , Norén G. Niklas , Onakpoya Igho J. 
Published: June 2024

AbstractIntroductionProduct information is intended to be a reference for healthcare professionals to verify instructions for monitoring and preventability of adverse drug reactions (ADRs), among other things. International comparisons of these documents, using the Systematic Information for Monitoring (SIM) method, have highlighted discrepancies in the instructions for monitoring, but there has been no comparison of preventability instructions.ObjectivesTo quantify and compare, across different countries, the completeness of instructions for monitoring and preventability provided to healthcare professionals in medicinal product information.MethodsWe shall retrieve information included with medicinal products that have been involved in signals communicated by regulators, in 2014–2019 and based on clinical assessments of reports of ADRs, from the websites of 35 regulatory agencies. We shall evaluate the completeness of instructions for monitoring using a modified version of the SIM method; a score of 67% will qualify a monitoring instruction as sufficiently complete. To evaluate the completeness of instructions for preventability, we have derived a framework from the Dose-responsiveness-Temporality-Susceptibility (DoTS) classification of ADRs and related implications, comprising domains and items/implications. We shall iteratively develop a threshold to define the sufficiency of completeness of instructions based on data distribution across DoTS domains. We shall present descriptive statistics by country for each item of the framework and by total scores, using tables, or figures where necessary.OutcomesOur target audience is regulators, and the results should highlight gaps in the level of information available to healthcare professionals. This study may also provide some insights into how suspicions of causality that arise from clinical assessments of reports of ADRs translate into actionable recommendations in clinical practice.
The Safety and Efficacy of Cangrelor in Endovascular Thrombectomy Compared with Glycoprotein IIb/IIIa Inhibitors
Authors: Devarajan Alex , Gottiparthi Shouri , Caton Michael T. , Ouf Aya , Wu Katty , Goldman Daryl , Davis Nicole , Musallam Nadine , Zhang Jack Y. , Rao Naina , Dangayach Neha , Davy Connor , Fara Michael , Majidi Shahram , Oxley Thomas , Kellner Christopher , Shigematsu Tomoyoshi , DeLeacy Reade , Mocco J , Fifi Johanna T. , Shoirah Hazem 
Published: June 2024

BackgroundCangrelor, an intravenous P2Y12-receptor inhibitor, is a reversible and short-acting antithrombotic medication non-inferior to irreversible Glycoprotein IIb-IIIa inhibitors (GPI) like eptifibatide. However, there is insufficient data to compare the medications in endovascular thrombectomy (EVT) cases requiring emergent platelet inhibition. This study reviews our experience with cangrelor in EVT and compares its safety and efficacy against GPIs.MethodsA large healthcare system retrospective review identified all patients who received cangrelor or eptifibatide intraoperatively during EVT from December 2018 to March 2023 for a cohort study. Clinical data was reviewed. Functional status was defined by the modified Rankin Scale (mRS) and National Institutes of Health Stroke Scale (NIHSS) at multiple time points. Binary variables were tested with Pearson χ2 tests or Fisher’s exact tests. Continuous variables were tested with two-tailed t-tests or Wilcoxon tests.ResultsOf 1,010 EVT patients, 36 cangrelor and 104 eptifibatide patients were selected. There were no significant differences in baseline functional status or presentations. Cangrelor was most frequently administered for stenting tandem occlusions (n=16, 44.4%) and successful reperfusion occurred in 93.3% of patients (n=30). On multivariate analysis, cangrelor usage was associated with decreased odds of hemorrhagic conversion (adjusted odds ratio (AOR) 0.76, p=0.004) and symptomatic hemorrhage (AOR 0.86, p=0.021). There were no significant differences in thrombotic re-occlusion. Cangrelor was associated with lower 24-hour NIHSS (7.0 vs. 12.0, p=0.013) and discharge NIHSS scores (3.0 vs 9.0, p=0.009). There were no significant differences in in-hospital mortality or length of stay. Cangrelor was associated with improved odds of favorable outcome, defined as mRS 0-2, at discharge (AOR 2.69, p=0.001) and on 90-day follow-up (AOR 2.23, p=0.031).ConclusionCangrelor was associated with a decreased risk of hemorrhagic conversion and may lead to favorable functional outcomes for patients during hospitalization when compared to GPIs. Future prospective studies are warranted to investigate its use in EVT.Previous PresentationsThis abstract was previous presented as a podium presentation at the Society of Neurointerventional Surgery’s 20thAnnual Meeting in San Diego, CA from July 31st- August 4th, 2023.
A novel variant inADPRSdisrupts ARH3 stability and subcellular localization in children with neurodegeneration and respiratory failure
Authors: Bannister Maxwell , Bray Sarah , Aggarwal Anjali , Billington Charles , Nguyen Hai Dang 
Published: June 2024

ABSTRACTPurposeADP-ribosylation is a post-translational modification involving the transfer of one or more ADP-ribose units from NAD+ to target proteins. Dysregulation of ADP-ribosylation is implicated in neurodegenerative diseases. Here we report a novel homozygous variant in theADPRSgene (c.545A>G, p.His182Arg) encoding the mono(ADP-ribosyl) hydrolase ARH3 found in 2 patients with childhood-onset neurodegeneration with stress-induced ataxia and seizures (CONDSIAS).MethodsGenetic testing via exome sequencing was used to identify the underlying disease cause in two siblings with developmental delay, seizures, progressive muscle weakness, and respiratory failure following an episodic course. Studies in a cell culture model uncover biochemical and cellular consequences of the identified genetic change.ResultsThe ARH3H182Rvariant affects a highly conserved residue in the active site of ARH3, leading to protein instability, degradation, and reduced expression. ARH3H182Radditionally fails to localize to the nucleus. The combination of reduced expression and mislocalization of ARH3H182Rresulted in accumulation of mono-ADP ribosylated species in cells.ConclusionsThe children’s clinical course combined with the biochemical characterization of their genetic variant develops our understanding of the pathogenic mechanisms driving CONDSIAS and highlights a critical role for ARH3-regulated ADP ribosylation in nervous system integrity.
Neuronal identity control at the resolution of a single transcription factor isoform
Authors: Smolin Natalie , Dombrovski Mark , Hina Bryce W. , Moreno-Sanchez Anthony , Gossart Ryan , Carmona Catherine R. , Rehan Aadil , Hussein Roni H. , Mirshahidi Parmis , Ausborn Jessica , Kurmangaliyev Yerbol Z. , von Reyn Catherine R. 
Published: June 2024

SUMMARYThe brain exhibits remarkable neuronal diversity which is critical for its functional integrity. From the sheer number of cell types emerging from extensive transcriptional, morphological, and connectome datasets, the question arises of how the brain is capable of generating so many unique identities. ‘Terminal selectors’ are transcription factors hypothesized to determine the final identity characteristics in post-mitotic cells. Which transcription factors function as terminal selectors and the level of control they exert over different terminal characteristics are not well defined. Here, we establish a novel role for the transcription factorbroadas a terminal selector inDrosophila melanogaster. We capitalize on existing large sequencing and connectomics datasets and employ a comprehensive characterization of terminal characteristics including Perturb-seq and whole-cell electrophysiology. We find a single isoformbroad-z4serves as the switch between the identity of two visual projection neurons LPLC1 and LPLC2.Broad-z4is natively expressed in LPLC1, and is capable of transforming the transcriptome, morphology, and functional connectivity of LPLC2 cells into LPLC1 cells when perturbed. Our comprehensive work establishes a single isoform as the smallest unit underlying an identity switch, which may serve as a conserved strategy replicated across developmental programs.
Targeting the paralog protein for degradation accounts for the opposite roles of NRBP1 and NRBP2 in regulating LINE1 retrotransposition
Authors: Yang Wei , Cong Shaobo , Schwarz Jennifer , Schulze Thilo , Ullrich Sara , Falkenstein Kristina , Ott Denis , Eixmann Pia , Trentino Angelica , Thien Antje , Heidmann Thierry , Schulze Ekkehard , Warscheid Bettina , Baumeister Ralf , Qi Wenjing 
Published: June 2024

SummaryGene duplication generates paralogs undergoing diverse fates during evolution and serves as a potent catalyst of biological complexity. Paralogs frequently share redundant functions and may also exhibit antagonistic activities by competing for common interaction partners. Here we show that the gene paralogsNRBP1andNRBP2oppositely regulate LINE1 retrotransposition, via influencing integrity of the LINE1 ribonucleoprotein complex. We demonstrate that the opposite roles of NRBP1 and NRBP2 are not results of a competitive mechanism, but rather due to targeting NRBP1 for proteasome-mediated decay by NRBP2, probably through heterodimer formation. Moreover, our phylogenetic analysis shows that the regulatory function of NRBP2 may be acquired later during evolution, suggesting that evolutionary pressure has favored this functional fine-tuning of NRBP1. In summary, our discovery not only identifies NRBP1/2 as novel LINE1 regulators and implicates their involvement in human pathogenesis, but also provides a novel insight into the regulatory details arising from gene duplication.
Detection of latent brain states from baseline neural activity in the amygdala
Authors: Aucoin Alexa , Lin Kevin K. , Gothard Katalin M. 
Published: June 2024

AbstractThe amygdala responds to a large variety of socially and emotionally salient environmental and interoceptive stimuli. The context in which these stimuli occur determines their social and emotional significance. In canonical neurophysiological studies, the fast-paced succession of stimuli and events induce phasic changes in neural activity. During inter-trial intervals neural activity is expected to return to a stable and relatively featureless baseline. Context, such as the presence of a social partner, or the similarity of trials in a blocked design, induces brain states that can transcend the fast-paced succession of stimuli and can be recovered from the baseline firing rate of neurons. Indeed, the baseline firing rates of neurons in the amygdala change between blocks of trials of gentle grooming touch, delivered by a trusted social partner, and non-social airflow stimuli, delivered by a computer-controlled air valve. In this experimental paradigm, the presence of the groomer alone was sufficient to induce small but significant changes in baseline firing rates. Here, we examine local field potentials (LFP) recorded during these baseline periods to determine whether context was encoded by network dynamics that emerge in the local field potentials from the activity of large ensembles of neurons. We found that machine learning techniques can reliably decode social vs. non-social context from spectrograms of baseline local field potentials. Notably, decoding accuracy improved significantly with access to broad-band information. No significant differences were detected between the nuclei of the amygdala that receive direct or indirect inputs from areas of the prefrontal cortex known to coordinate flexible, context-dependent behaviors. The lack of nuclear specificity suggests that context-related synaptic inputs arise from a shared source, possibly interoceptive inputs that signal the sympathetic- vs. parasympathetic-dominated states characterizing non-social and social blocks, respectively.
Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody
Authors: Pinto Torres Joar Esteban , Claes Mathieu , Hendrickx Rik , Yuan Meng , Smiejkowska Natalia , Van Wielendaele Pieter , Hacisuleyman Aysima , De Winter Hans , Muyldermans Serge , Michels Paul A. , Walkinshaw Malcolm D. , Versées Wim , Caljon Guy , Magez Stefan , Sterckx Yann G.-J. 
Published: June 2024

AbstractAfrican trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.
TS-AI: A deep learning pipeline for multimodal subject-specific parcellation with task contrasts synthesis
Authors: Li Chengyi , Lu Yuheng , Yu Shan , Cui Yue 
Published: June 2024

AbstractAccurate mapping of brain functional subregions at an individual level is crucial. Task-based functional MRI (tfMRI) captures subject-specific activation patterns during various functions and behaviors, facilitating the individual localization of functionally distinct subregions. However, acquiring high-quality tfMRI is time-consuming and resource-intensive in both scientific and clinical settings. The present study proposes a two-stage network model, TS-AI, to individualize an atlas on cortical surfaces through the prediction of tfMRI data. TS-AI first synthesizes a battery of task contrast maps for each individual by leveraging tract-wise anatomical connectivity and resting-state networks. These synthesized maps, along with feature maps of tract-wise anatomical connectivity and resting-state networks, are then fed into an end-to-end deep neural network to individualize an atlas. TS-AI enables the synthesized task contrast maps to be used in individual parcellation without the acquisition of actual task fMRI scans. In addition, a novel feature consistency loss is designed to assign vertices with similar features to the same parcel, which increases individual specificity and mitigates overfitting risks caused by the absence of individual parcellation ground truth. The individualized parcellations were validated by assessing test-retest reliability, homogeneity, and cognitive behavior prediction using diverse reference atlases and datasets, demonstrating the superior performance and generalizability of TS-AI. Sensitivity analysis yielded insights into region-specific features influencing individual variation in functional regionalization. In addition, TS-AI identified accelerated shrinkage in the medial temporal and cingulate parcels during the progression of Alzheimer’s disease, suggesting its potential in clinical research and applications.
A spatiotemporally resolved GPCR interactome reveals novel mediators of receptor agonism
Authors: Shchepinova Maria M. , Richardson Rachel , Houghton Jack W. , Walker Abigail R. , Conole Daniel , Hanyaloglu Aylin C. , Tate Edward W. 
Published: June 2024

SummaryCellular signaling by membrane G protein-coupled receptors (GPCRs) is orchestrated by a complex and diverse array of mechanisms. The dynamics of a GPCR interactome as it evolves over time and space in response to an agonist can offer a unique window on pleiotropic signaling decoding and functional selectivity at a cellular level. In this study, we employed proximity-based APEX2 proteomics to interrogate the interaction network of the GPCR for luteinizing hormone (LHR) on a sub-minute timescale. We developed an analytical approach integrating quantitative multiplexed proteomics and temporal reference profiles, providing a platform to identify the proteomic environment of APEX2-tagged LHR at the nanometer scale. LHR activity is exquisitely regulated at a spatial level, leading to identification of novel interactors including the Ras-related GTPase RAP2B that modulate both receptor signaling and post-endocytic trafficking, and providing a resource for spatiotemporal nanodomain mapping of LHR interactors across subcellular compartments.
FINCA disease mouse model exhibits altered behaviour and immune response
Authors: Hiltunen Anniina E. , Kangas Salla M. , Gondane Aishwarya , Koivisto Henna , Salokas Kari , Heikkinen Anne , Salo Miia H. , Röning Tapio , Tallgren Antti , Glumoff Virpi , Denis Maria C. , Karagianni Niki , Myllyharju Johanna , Varjosalo Markku , Tanila Heikki , Itkonen Harri M. , Rämet Mika , Uusimaa Johanna , Hinttala Reetta 
Published: June 2024

AbstractFibrosis, neurodegeneration and cerebral angiomatosis (FINCA) is a childhood-onset multi-organ neurodevelopmental disorder associated with multi-organ manifestations and recurrent infections. The disease is caused by variants inNHLRC2initiating a cascade of unknown pathological events. Previously, we have demonstrated that despite the significant decrease at the molecular level, the compound heterozygosity of knock out and p.Asp148Tyr alleles in NHLRC2 does not lead to a severe phenotype in mice. Here, we analysed the behavioural and immunological phenotype of the FINCA mice and studied the molecular pathways affected by p.Asp148Tyr in NHLRC2 using mouse and human-derived cell culture models. The FINCA mice displayed a mild hyperactivity and deficient early immune response when challenged with LPS leading to altered cytokine responses, including IFNγ, IL-12, and TNFα. By comparing gene expression and putative interaction partners affected by p.Asp148Tyr, we identified Rho GTPase signalling as the common pathway. Altogether, these results establish a multi-dimensional impact of the p.Asp148Tyr variant in NHLRC2. Knowledge of the molecular pathways affected by NHLRC2 and the natural course of FINCA disease progression are instrumental for the development of effective therapeutics.Summary statementFINCA is a paediatric neurodevelopmental and multi-organ disorder caused by variants inNHLRC2. Here, mild hyperactivity in connection with altered early immune response is described in the FINCA mouse model.