bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel high throughput microwell outgrowth assay for HIV infected cells
Authors: Fenton Anthony D , Archin Nancie , Turner Anne-Marie , Joseph Sarah , Moeser Matthew , Margolis David M , Browne Edward P 
Published: October 2023

AbstractAlthough antiretroviral therapy (ART) is highly effective at suppressing HIV replication, a viral reservoir persists that can reseed infection if ART is interrupted. Curing HIV will require elimination or functional containment of this reservoir, but the size of the HIV reservoir is highly variable between individuals. To evaluate the overall size of the HIV reservoir, several assays have been developed, including PCR based assays for viral DNA, the Intact Proviral DNA Assay (IPDA), and the Quantitative Viral Outgrowth Assay (QVOA). QVOA is the gold standard assay for measuring inducible replication competent proviruses, but this assay is technically challenging and time consuming. To provide a more rapid and less laborious tool for quantifying cells infected with replication competent HIV, we developed the Microwell Outgrowth Assay (MOA), in which HIV infected CD4 T cells are cocultured with an HIV-detecting reporter cell line in a polydimethylsiloxane (PDMS)/polystyrene array of nanoliter sized wells (rafts). Transmission of HIV from infected cells to the reporter cell line induces fluorescent reporter protein expression that is detected by automated scanning across the array. We show that this assay can detect HIV infected cells with a high degree of sensitivity and precision. Using this approach, we were able to detect HIV infected cells from ART-naïve people with HIV (PWH) and from PWH on ART. Furthermore, we demonstrate that infected cells can be recovered from individual rafts and used to analyze the diversity of viral sequences. This assay may be a useful tool for quantifying and characterizing infected cells from PWH.Author summaryMeasuring the size of the HIV reservoir in people with HIV (PWH) will be important for determining the impact of HIV cure strategies. However, measuring this reservoir is challenging. We report a new method for quantifying HIV infected cells that involves culturing cells from PWH in an array of microwells with a cell line that detects HIV infection. We show that this approach can detect rare HIV infected cells and derive detailed virus sequence information for each infected cell.
Differences in white matter detected byex vivo9.4T MRI are associated with axonal changes in the R6/1 model of Huntington’s Disease
Authors: Casella C. , Kelly B. , Murillo Bartolome A. , Mills-Smith B. , Parker G.D. , Von Ruhland C. , Syed Y.A. , Dion V. , Rosser A.E. , Metzler-Baddeley C. , Jones D.K. , Lelos M.J. 
Published: October 2023

AbstractWhite matter (WM) volume loss has been reported in people with Huntington’s disease (HD), but the cellular basis of this deficit remains to be elucidated. To address this, we assessed ex vivo WM microstructure in the transgenic R6/1 mouse model of HD with magnetic resonance imaging (MRI) and studied the neurobiological basis of the MRI brain signals with histological and electron microscopy analyses in a separate cohort of age- and sex-matched mice. Differences in the macromolecular proton fraction (MPF) from quantitative magnetization transfer (qMT) as a proxy myelin measure, and the intra-axonal signal fraction (FR) from the composite hindered and restricted model of diffusion (CHARMED) as a proxy marker of axon density, were assessed alongside diffusion tensor imaging (DTI) parameters. A tractometry approach was employed to inspect region-specific differences across the corpus callosum (CC). Furthermore, voxel-based morphometry (VBM) and tract-based spatial statistics (TBSS) were used to explore brain-wise WM macro- and microstructure abnormalities. To gain insight into disease-associated impairments in attentional and visuospatial processing, a third cohort of age-matched mice was assessed with the 5-choice serial reaction time task (5-CSRTT). We report cognitive impairments in R6/1 mice and, by evaluating MRI and light and electron microscopy results, we show that this HD mouse model presents disruptions in axonal morphology (i.e. less complex, thinner axons) and organization (i.e. more densely packed axons). Furthermore, we show that, at least early in disease progression, R6/1 mice present a reduction in the expression or content of myelin-associated proteins without significant alterations in the structure of myelin sheaths. Finally, our findings indicate that neuroinflammation-driven glial and axonal swelling might also affect this mouse model early in disease progression. Crucially, we demonstrate the potential of FR, an in vivo estimate of axon density, as a novel MRI biomarker of HD-associated changes in WM microstructure.
Region-specific gene expression changes associated to oleoylethanolamide-induced attenuation of alcohol self-administration
Authors: González-Portilla Macarena , Montagud-Romero Sandra , Mellado Susana , Rodríguez de Fonseca Fernando , Pascual María , Rodríguez-Arias Marta 
Published: October 2023

AbstractOleoylethanolamide (OEA) is a lipid with anti-inflammatory activity that modulates multiple reward-related behaviors. Previous studies have shown that OEA treatment reduces alcohol self-administration (SA) while inhibiting alcohol-induced inflammatory signaling. Nevertheless, the specific mechanisms that OEA is targeting to achieve these effects have not been widely explored. Here, we tested the effects of OEA treatment during alcohol SA, extinction or previous to cue-induced reinstatement of alcohol seeking. In addition, we measured gene expression changes in the striatum and hippocampus of relevant receptors for alcohol consumption (DrD1, DrD2, CNR1, OPRM1) as well as immune-related proteins (IL-6, IL-1β, TLR4) and the brain-derived neurotrophic factor (BDNF). Our results confirmed that when administered contingently, systemic OEA administration reduced alcohol SA and attenuated cue-induced reinstatement. Interestingly, we also observed that OEA treatment reduced the number of sessions needed for extinction of alcohol seeking. Biochemical analyses showed region-specific OEA dopaminergic and cannabinoid receptor gene expression alterations. Also, OEA treatment modulated the long-term immune response and increased BDNF expression. These results suggest that boosting OEA levels may be an effective strategy for reducing alcohol SA and preventing relapse.
De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout ofBbs1
Authors: Freke Grace , Martins Tiago , Davies Rosie , Beyer Tina , Seda Marian , Peskett Emma , Haq Naila , Prasai Avishek , Otto Georg , Srikaran Jeshmi Jeyabalan , Hernandez Victor , Diwan Gaurav , Russell Robert , Ueffing Marius , Huranova Martina , Boldt Karsten , Beales Philip L. , Jenkins Dagan 
Published: October 2023

AbstractBardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue specific, and gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane trafficking and intraflagellar transport (IFT) adaptor protein complex formed by 8 BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations inBbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically-defined clones. Our results suggest that BBS1 is required for suppression of mesenchymal cell identities as IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, and BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively this work suggests that the dynamic stability of the BBSome is essential for suppression of mesenchymal cell identities as epithelial cells differentiate.
Recognition of the Nucleotide-Dependent Feature Facilitates the Microtubule End-Binding of MCAK
Authors: Chen Wei , Song Yin-Long , He Jian-Feng , Liang Xin 
Published: October 2023

AbstractThe growing plus-end is a key regulatory site for microtubule dynamics. MCAK (mitotic centromere-associated kinesin), a microtubule depolymerizing kinesin, is an end-binding regulator of catastrophe frequency. It is intriguing how MCAK specifically binds to dynamic microtubule ends. Here, we measure the end-binding kinetics of MCAK using single-molecule imaging and reveal the end-binding preference. MCAK binds to the entire GTP cap, including the EB cap and the distalmost cap. Further analysis shows that MCAK strongly binds to GTPγS microtubules, suggesting that it could recognize the nucleotide-dependent feature of microtubules. Moreover, the binding preference is independent on the nucleotide state of MCAK, and this feature facilitates the high-affinity end-binding of MCAK. Finally, we show that despite partially sharing the binding regions, MCAK and XMAP215 function in an additive manner, demonstrating a simple logic of how the end-binding regulators work in co-ordination. In all, our results provide novel insights into understanding how MCAK regulates the dynamics of microtubule ends.
Robustness and adaptability of sensorimotor skills in expert piano performance
Authors: Yasuhara Masaki , Uehara Kazumasa , Oku Takanori , Shiotani Sachiko , Nambu Isao , Furuya Shinichi 
Published: October 2023

AbstractSkillful execution of sequential actions requires the delicate balance of sensorimotor control, encompassing both robustness and adaptability. Previous studies have characterized behavioral and electrophysiological responses to sensory perturbation during performance of sequential movements such as speech and singing. However, it remains unknown whether and in what manner both motor and neural responses, triggered by sensory perturbation, undergo plastic adaptation as a consequence of extensive sensorimotor experience. Here, we addressed this question by comparing effects of transiently delayed tone production on the spatiotemporal patterns of the subsequent motor actions and event-related potentials (ERPs) during fast and accurate piano performance between expert pianists and musically-untrained individuals (non-musicians). Following the delayed tone production, the inter-keystroke interval was abnormally prolonged in non-musicians but not in pianists. By contrast, the keystroke velocity following the tone delay was increased only in the pianists. A regression model further demonstrated that the change in the inter-keystroke interval following the perturbation covaried with the ERPs of the N180 and P300 components particularly at the frontal and parietal regions. In contrast, the alteration in the keystroke velocity was associated with the P300 component of the temporal region ipsilateral to the moving hand, which suggests enhancement of auditory but not somatosensory feedback gain following auditory perturbation. Together, these findings suggest that distinct neural mechanisms underlie robust and adaptive sensorimotor skills individuals with different levels of proficiency.
hiPSC-CM Electrophysiology: Impact of Temporal Changes and Study Parameters on Experimental Reproducibility
Authors: Guerrelli Devon , Pressman Jenna , Posnack Nikki 
Published: October 2023

AbstractHuman induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are frequently used for preclinical cardiotoxicity testing and remain an important tool for confirming model-based predictions of drug effects in accordance with the Comprehensivein VitroProarrhythmia Assay (CiPA) initiative. Despite the considerable benefits hiPSC-CMs provide, concerns surrounding experimental reproducibility have emerged. Our study aimed to investigate the effects of temporal changes and experimental parameters on hiPSC-CM electrophysiology. hiPSC-CMs (iCell cardiomyocyte2) were cultured for 14 days and biosignals were acquired using a microelectrode array (MEA) system. Continuous recordings revealed a 22.6% increase in the beating rate and 7.7% decrease in the field potential duration (FPD) during a 20-minute equilibration period. Location specific differences across a multiwell plate were also observed, with hiPSC-CMs in the outer rows beating 8.8 beats per minute (BPM) faster than the inner rows. Cardiac endpoints were also impacted by cell culture duration; from 2-14 days the beating rate decreased (–12.7 BPM), FPD lengthened (+257 ms), and spike amplitude increased (+3.3 mV). Cell culture duration (4-10 days) also impacted hiPSC-CM drug responsiveness (E-4031, nifedipine, isoproterenol). Our study highlights multiple sources of variability that should be considered and addressed when performing hiPSC-CM MEA studies. To improve reproducibility and data interpretation, MEA-based studies should establish a standardized protocol and report key experimental conditions (e.g., culture time, equilibration time, electrical stimulation settings, report raw data values).New & NoteworthyWe demonstrate that hiPSC-CM electrophysiology measurements are significantly impacted by slight deviations in experimental techniques including electrical stimulation protocols, equilibration time, well-to-well variability, and length of hiPSC-CM culture. Furthermore, our results indicate that hiPSC-CM drug responsiveness changes within the first two weeks following defrost.Graphical AbstractImage created with Biorender.com
Biocalcification in porcelaneous foraminifera
Authors: Dubicka Zofia , Tyszka Jarosław , Pałczyńska Agnieszka , Höhne Michelle , Bijma Jelle , Janse Max , Klerks Nienke , Bickmeyer Ulf 
Published: October 2023

AbstractLiving organisms control the formation of mineral skeletons and other structures through biomineralization. Major phylogenetic groups usually consistently follow a single biomineralization pathway. Foraminifera, which are very efficient marine calcifiers, making a substantial contribution to global carbonate production and global carbon sequestration, are regarded as an exception. This phylum has been commonly thought to follow two contrasting models of eitherin situ“mineralization of extracellular matrix” attributed to hyaline rotaliid shells, or “mineralization within intracellular vesicles” attributed to porcelaneous miliolid shells. Our previous results on rotaliids along with those on miliolids in this paper question such a wide divergence of biomineralization pathways within the same phylum of Foraminifera. We found that both groups produced calcareous shells via the intravesicular formation of unstable mineral precursors (Mg-rich amorphous calcium carbonates) supplied by endocytosed seawater and deposited at the site of new wall formation within the organic matrix. Precipitation of high-Mg calcitic mesocrystals took placein situand formed a dense, chaotic meshwork of needle-like crystallites. We did not observe deposition of calcified needles that had already precipitated in the transported vesicles, which challenges the previous model of miliolid mineralization. Hence, Foraminifera utilize less divergent calcification pathways, following the recently discovered biomineralization principles. Mesocrystalline chamber walls are therefore apparently created by accumulating and assembling particles of pre-formed liquid amorphous mineral phase within the extracellular organic matrix enclosed in a biologically controlled privileged space by active pseudopodial structures. Both calcification pathways evolved independently in the Paleozoic and are well-conserved in two clades that represent different chamber formation modes.
Tapping into the nativePseudomonasBacterial Biofilm Structure by High-Resolution 1D and 2D MAS solid-state NMR
Authors: Byeon Chang-Hyeock , Kinney Ted , Saricayir Hakan , Srinivasa Sadhana , Wells Meghan K. , Kim Wook , Akbey Ümit 
Published: October 2023

AbstractWe present a high-resolution 1D and 2D magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nativePseudomonas fluorescenscolony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D1H-13C ssNMR spectrum and thorough peak deconvolution approach at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT13C ssNMR spectra to different signals originating from the mobile and rigid fractions of the biofilm, and qualitative determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC signals as a template, a biofilm forming functional amyloid fromPseudomonas. We also attempted to identify biofilm polysaccharide species by using1H/13C chemical shifts obtained from the 2D spectrum. This study marks the first demonstration of high-resolution 2D ssNMR spectroscopy for characterizing native bacterial biofilms and expands the scope of ssNMR in studying biofilms. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.
Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants ofSaccharomyces cerevisiae
Authors: Kundnani Deepali L. , Yang Taehwan , Gombolay Alli L. , Mukherjee Kuntal , Newnam Gary , Meers Chance , Mehta Zeel H. , Mouawad Celine , Storici Francesca 
Published: October 2023

SUMMARYRibonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered two AGS-ortholog mutations inSaccharomyces cerevisiae:rnh201-G42S andrnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these yeast AGS-ortholog mutants. We found higher rNMP incorporation in the nuclear genome ofrnh201-G42S than in wild-type andrnh203-K46W-mutant cells, and an elevated rCMP content in both mutants. Moreover, we uncovered unique rNMP patterns in each mutant, highlighting a differential activity of the AGS mutants towards rNMPs embedded on the leading or on the lagging strand of DNA replication. This study guides future research on rNMP characteristics in human genomic samples carrying AGS mutations.
Building on-chip cytoskeletal circuits via branched microtubule networks
Authors: Zaferani Meisam , Song Ryungeun , Petry Sabine , Stone Howard A. 
Published: October 2023

AbstractControllable platforms to engineer robust cytoskeletal scaffolds have the potential to create novel on-chip nanotechnologies. Inspired by axons, we combined the branching microtubule (MT) nucleation pathway with microfabrication to develop “cytoskeletal circuits”. This active matter platform allows control over the adaptive self-organization of uniformly polarized MT arrays via geometric features of microstructures designed within a microfluidic confinement. We build and characterize basic elements, including turns and divisions, as well as complex regulatory elements, such as biased division and MT diodes, to construct various MT architectures on a chip. Our platform could be used in diverse applications, ranging from efficient on-chip molecular transport to mechanical nano-actuators. Further, cytoskeletal circuits can serve as a tool to study how the physical environment contributes to MT architecture in living cells.SignificanceMicrotubules have essential functions within the cell, including providing a robust railroad for motor-driven cargo transport. The unique properties of microtubules have stimulated attempts to harness these characteristics for targeted delivery of molecular complexes, novel material design, and developing nanotechnologies with precision comparable to living organisms. However, Previous efforts mainly focused on microtubules with fixed length and layout and no controlled MT generation, setting a limit on designing MT architecture. In this study, we integrated nanofabrication with microtubule branching reactions borrowed directly from the cell’s toolkit to construct cytoskeletal circuits and generate microtubule architectures from scratch. That is, our system enables control over microtubule growth and autocatalytic nucleation on a microfluidic chip with micro/nanostructures patterned within.
Cytochrome P450 and Epoxide Hydrolase Metabolites in Aβ and tau-induced Neurodegeneration: Insights fromCaenorhabditis elegans
Authors: Sarparast Morteza , Hinman Jennifer , Pourmand Elham , Vonarx Derek , Ramirez Leslie , Ma Wenjuan , Liachko Nicole F. , Alan Jamie K. , Lee Kin Sing Stephen 
Published: October 2023

ABSTRACTThis study aims to uncover potent cytochrome P450 (CYP) and epoxide hydrolase (EH) metabolites implicated in Aβ and/or tau-induced neurodegeneration, independent of neuroinflammation, by utilizingCaenorhabditis elegans(C. elegans) as a model organism. Our research reveals that Aβ and/or tau expression inC. elegansdisrupts the oxylipin profile, and epoxide hydrolase inhibition alleviates the ensuing neurodegeneration, likely through elevating the epoxy-to-hydroxy ratio of various CYP-EH metabolites. In addition, our results indicated that the Aβ and tau likely affect the CYP-EH metabolism of PUFA through different mechanism. These findings emphasize the intriguing relationship between lipid metabolites and neurodegenerations, in particular, those linked to Aβ and/or tau aggregation. Furthermore, our investigation sheds light on the crucial and captivating role of CYP PUFA metabolites inC. elegansphysiology, opening up possibilities for broader implications in mammalian and human contexts.Abstract Figure
Host plant odour and sex pheromone are integral to mate finding in codling moth
Authors: Erdei Anna , Preti Michele , Bengtsson Marie , Witzgall Peter 
Published: October 2023

AbstractBehaviour-modifying chemicals mediate sexual communication and host choice in insect herbivores. Sex pheromones are believed to attract insects by themselves, even though they are released into an atmosphere of plant odorants. We show for the first time that, in codling moth, feeding on apple and pear, that female pheromone is efficient for male attraction only in the presence of host plant odour. In non-host vegetation, male attraction to sex pheromone was very strongly reduced. The role of host odour in sex attraction was then substantiated by blending synthetic pheromone, codlemone, and the kairomone pear ester, a strong host plant attractant. An admixture of pear ester entirely rescued pheromone attraction in non-host vegetation. This field behavioural assay substantiates that host plant olfactory cues are integral part of sexual communication and mate recognition, which provides a mechanism for how shifts to new host plants produce new mate recognition signals.