bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Fluorescence Microscopy (iFLM) for Cryo-FIB-milling and In-situ Cryo-ET
Authors: Yang Jae , Vrbovská Veronika , Franke Tilman , Sibert Bryan , Larson Matthew , Hall Alex , Rigort Alex , Mitchels John , Wright Elizabeth R. 
Published: July 2023

AbstractCorrelative cryo-FLM-FIB milling is a powerful sample preparation technique forin situcryo-ET. However, correlative workflows that incorporate precise targeting remain challenging. Here, we demonstrate the development and use of an integrated Fluorescence Light Microscope (iFLM) module within a cryo-FIB-SEM to enable a coordinate-based two-point 3D correlative workflow. The iFLM guided targeting of regions of interest coupled with an automated milling process of the cryo-FIB-SEM instrument allows for the efficient preparation of 9-12 ∼200 nm thick lamellae within 24 hours. Using regular and montage-cryo-ET data collection schemes, we acquired data from FIB-milled lamellae of HeLa cells to examine cellular ultrastructure. Overall, this workflow facilitates on-the-fly targeting and automated FIB-milling of cryo-preserved cells, bacteria, and possibly high pressure frozen tissue, to produce lamellae for downstream cryo-ET data collection.
Multi-tissue proteomics identifies a link between satellite DNA organization and heritable transposon repression inDrosophila
Authors: Chavan Ankita , Skrutl Lena , Uliana Federico , Pfister Melanie , Brändle Franziska , Tirian Laszlo , Baptista Delora , Handler Dominik , Burke David , Sintsova Anna , Beltrao Pedro , Brennecke Julius , Jagannathan Madhav 
Published: July 2023

ABSTRACTNon-coding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. Despite the pivotal role of chromocenters in cellular processes like genome encapsulation and gene repression, the associated proteins remain incompletely characterized. Here, we use two satellite DNA-binding proteins, D1 and Prod, as baits to characterize the chromocenter-associated proteome in Drosophila embryos, ovaries, and testes through quantitative mass spectrometry. We identify D1- and Prod-associated proteins, including known heterochromatin proteins as well as proteins previously unlinked to satellite DNA or chromocenters, thereby laying the foundation for a comprehensive understanding of cellular functions enabled by satellite DNA repeats and their associated proteins. Interestingly, we find that multiple components of the transposon-silencing piRNA pathway are associated with D1 and Prod in embryos. Using genetics, transcriptomics, and small RNA profiling, we show that flies lacking D1 during embryogenesis exhibit transposon expression and gonadal atrophy as adults. We further demonstrate that this gonadal atrophy can be rescued by mutating the checkpoint kinase, Chk2, which mediates germ cell arrest in response to transposon mobilization. Thus, we reveal that a satellite DNA-binding protein functions during embryogenesis to silence transposons, in a manner that is heritable across later stages of development.
Female-biased expressed odorant receptor genes differentially tuned to repulsive or attractive plant volatile compounds in the turnip moths
Authors: Zhang Dan-Dan , Hou Xiao-Qing , Powell Daniel , Löfstedt Christer 
Published: July 2023

AbstractInsects rely on their highly efficient and precise olfactory systems to find suitable mates, host plants and oviposition sites, and adapt to the changing environment. The odorant receptors (ORs) including pheromone receptors (PRs) play a vital role in this process. While extensive studies have been focusing on deorphanization of lepidopteran PR genes, the information on the ligand profiles of general ORs is still sparse. In the present study, we identified a repertoire of 61 ORs including the co-receptor Orco from antennal and ovipositor transcriptomes of the turnip mothAgrotis segetum, which clustered in all the major lepidopteran OR clades. We characterized the function of eight female-biased expressed ORs inXenopusoocytes and found three ORs differentially tuned to plant volatile compounds that might be repulsive or attractive to the moths. AsegOR13 was broadly tuned to a number of herbivore-induced plant volatiles (HIPVs) while AsegOR20 was specific to citral; AsegOR17 was narrowly tuned to the alcohols, isoamyl alcohol, pentanol and benzyl alcohol, that are potentially attractive to moths. The orthologues of the three ORs in other moth species seem to share the conserved function. Our results support the hypothesis that insects recognize their host plants mostly by detecting the mixture of ubiquitous compounds, instead of taxonomically characteristic host compounds. The combination of narrowly and broadly tuned ORs will ensure both the accuracy of the most important odor signals and the plasticity of the olfactory system to the changes in the environment.
Misperceiving momentum: computational mechanisms of biased striatal reward prediction errors in bipolar disorder
Authors: Moningka Hestia , El-Deredy Wael , Bentall Richard P , Mason Liam 
Published: July 2023

AbstractBackgroundDysregulated reward processing and mood instability are core features of bipolar disorder that have largely been considered separately, and with contradictory findings. We sought to test a mechanistic account that proposes that, in bipolar disorder, there is an excessive tendency to enter recursive cycles in which reward perception is biased by signals that the environment might be changing for the better or worse.MethodsParticipants completed a probabilistic reward task with functional Magnetic Resonance Imaging. Using an influential computational model, we ascertained whether participants with bipolar disorder (n= 21) show greater striatal tracking of momentum-biased reward prediction errors (RPEs) than healthy controls (n= 21). We conducted psychophysiological interaction analyses to quantify the degree to which each group modulated functional connectivity between the ventral striatum and left anterior insula in response to fluctuations in momentum.ResultsIn the bipolar disorder group, but not controls, the momentum-biased RPE model accounted for significant additional variance in ventral striatal activity beyond a standard mode of veridical RPEs. Compared to controls, the bipolar disorder group exhibited lower ventral striatal-left insular functional connectivity modulated by momentum-biased RPE. Moreover, this reduction in connectivity was more pronounced as a function of current manic symptoms.ConclusionsConsistent with an existing theory, we found evidence that bipolar disorder is associated with a tendency for momentum to excessively bias striatal tracking of RPE signals. We identify impaired striatal-insular connectivity as a possible locus for this propensity. We argue that computational psychiatric approaches that examine momentary shifts in reward and mood dynamics have strong potential for new mechanistic insights and targets for intervention.
MYCN driven oncogenesis involves cooperation with WDR5 to activate canonical MYC targets and G9a to repress differentiation genes
Authors: Liu Zhihui , Zhang Xiyuan , Xu Man , Hong Jason J. , Ciardiello Amanda , Lei Haiyan , Shern Jack F. , Thiele Carol J. 
Published: July 2023

AbstractMYCN activates canonical MYC targets involved in ribosome biogenesis, protein synthesis and represses neuronal differentiation genes to drive oncogenesis in neuroblastoma (NB). How MYCN orchestrates global gene expression remains incompletely understood. Our study finds that MYCN binds promoters to up-regulate canonical MYC targets but binds to both enhancers and promoters to repress differentiation genes. MYCN-binding also increases H3K4me3 and H3K27ac on canonical MYC target promoters and decreases H3K27ac on neuronal differentiation gene enhancers and promoters. WDR5 is needed to facilitate MYCN promoter binding to activate canonical MYC target genes, whereas MYCN recruits G9a to enhancers to repress neuronal differentiation genes. Targeting both MYCN’s active and repressive transcriptional activities using both WDR5 and G9a inhibitors synergistically suppresses NB growth. We demonstrate that MYCN cooperates with WDR5 and G9a to orchestrate global gene transcription. The targeting of both these cofactors is a novel therapeutic strategy to indirectly target the oncogenic activity ofMYCN.
Hip strengthening exercise dosage is not associated with clinical improvements after total hip arthroplasty – a prospective cohort study (the PHETHAS-1 study)
Authors: Madsen Merete Nørgaard , Mikkelsen Lone Ramer , Rathleff Michael Skovdal , Thorborg Kristian , Kallemose Thomas , Bandholm Thomas 
Published: July 2023

AbstractPurposePostoperative rehabilitation exercise is commonly prescribed after total hip arthroplasty (THA), but its efficacy compared to no or minimal rehabilitation exercise has been questioned. Preliminary efficacy would be indicated if a dose-response relationship exists between performed exercise dose and degree of postoperative recovery. The objective was to evaluate the preliminary efficacy of home-based rehabilitation using elastic band exercise on performance-based function after THA, based on the association between performed exercise dose and change in performance-based function (gait speed) from 3 (start of intervention) to 10 weeks (end of intervention) after surgery.MethodsA pre-registered (NCT03109821) prospective cohort study was conducted. Following primary THA, patients were prescribed home-based rehabilitation exercise using elastic bands. Performed exercise dose (repetitions/week) was objectively measured using attached sensor technology. Primary outcome was change in gait speed (40m fast-paced walk test). Secondary outcomes included patient-reported hip disability. In the primary analysis, a linear regression model was used.ResultsNinety-four patients (39 women) with a median age of 66.5 years performed a median of 339 exercise repetitions/week (1st-3rd quartile: 209-549). Across outcomes, participants significantly improved from 3 to 10-week follow-up. The association between performed exercise dose and change in mean gait speed was 0.01 m/sec [95% CI: -0.01; 0.02] per 100 repetitions.ConclusionsWe found no indication of preliminary efficacy of home-based rehabilitation exercise using elastic bands, as no significant and clinically relevant associations between performed exercise dose and changes in outcomes were present. Trials comparing postoperative rehabilitation exercise with no exercise early after THA are warranted.
Digital Exclusion as a barrier to accessing healthcare: A summary composite indicator and online tool to explore and quantify local differences in levels of exclusion
Authors: Mee Paul , Gussy Mark , Huntley Phil , Kenny Amanda , Jarratt Theo , Kenward Nigel , Ward Derek , Vaughan Aiden 
Published: July 2023

AbstractExisting disparities in digital access were exacerbated with the accelerated shift to online provision of services during the COVID-19 pandemic, particularly for already disadvantaged groups. Metrics to quantify relative local differences in levels of digital exclusion are a necessary pre-requisite for the targeting of interventions to address these disparities. In this study we developed a composite indicator and an interactive dashboard ‘The Lincolnshire Digital Health Toolkit’ to explore digital exclusion in Lincolnshire, UK. To develop the indicator, individual variables were normalised and aggregated, intra-variable correlations explored, and factor analysis used to determine variable weightings. Three underlying factors were identified that explained a significant proportion of the variance in the original variables, the first two predominantly related to socioeconomic deprivation and lack of activity. In general, coastal areas in the east of the county had higher levels of digital exclusion, with significant local variation particularly within urban areas. Long travel times to reach medical facilities are an additional barrier in some communities. The toolkit has been used to support the evidence-based geographic targeting of interventions to address barriers to accessing digitally based health information and services. The impact of digital exclusion must be addressed to reduce marginalisation and isolation. The Lincolnshire Digital Health Toolkit provides a novel composite metric tailored to the conditions of this largely rural county and an interactive dashboard to support decisions on resource allocation.
ATUM-Tomo: A multi-scale approach to cellular ultrastructure by combined volume scanning electron microscopy and electron tomography
Authors: Kislinger Georg , Fabig Gunar , Wehn Antonia , Rodriguez Lucia , Jiang Hanyi , Niemann Cornelia , Klymchenko Andrey S. , Plesnila Nikolaus , Misgeld Thomas , Müller-Reichert Thomas , Khalin Igor , Schifferer Martina 
Published: July 2023

AbstractLike other volume electron microscopy approaches, Automated Tape Collecting Ultramicrotomy (ATUM) enables imaging of serial sections deposited on thick plastic tapes by scanning electron microscopy (SEM). ATUM is unique in enabling hierarchical imaging and thus efficient screening for target structures, as needed for correlative light and electron microscopy. However, SEM of sections on tape can only access the section surface, thereby limiting the axial resolution to the typical size of cellular vesicles with an order of magnitude lower than the acquired xy resolution. In contrast, serial-section electron tomography (ET), a transmission electron microscopy-based approach, yields isotropic voxels at full EM resolution, but requires deposition of sections on electron-stable thin and fragile films, thus making screening of large section libraries difficult and prone to section loss. To combine the strength of both approaches, we developed ‘ATUM-Tomo’, a hybrid method, where sections are first reversibly attached to plastic tape via a dissolvable coating, and after screening detached and transferred to the ET-compatible thin films. ATUM-SEM of serial semi-thick sections and consecutive ET of selected re-mounted sections combines SEM’s fast target recognition and coarse rendering capability with high-resolution volume visualizations, respectively, thus enabling multi-scale interrogation of cellular ultrastructure. As a proof-of-principle, we applied correlative ATUM-Tomo to study ultrastructural features of blood brain barrier (BBB) leakiness around microthrombi in a mouse model of traumatic brain injury. Microthrombi and associated sites of BBB leakiness were identified by confocal imaging of injected fluorescent and electron-dense nanoparticles, then relocalized by ATUM-SEM, and finally interrogated by correlative ATUM-Tomo. This workflow is a seamless zoom-in on structural BBB pathology from the micro- to the nanometer scale. Overall, our new ATUM-Tomo approach will substantially advance ultrastructural analysis of biological phenomena that require cell- and tissue-level contextualization of the finest subcellular textures.
Fungal-bacterial gut microbiota interactions in patients withClostridioides difficilecolonisation and infection
Authors: Henderickx Jannie G.E. , Crobach Monique J.T. , Terveer Elisabeth M. , Smits Wiep Klaas , Kuijper Ed J. , Zwittink Romy D. 
Published: July 2023

AbstractObjectivesThe bacterial microbiota is well-recognised for its role inClostridioides difficilecolonisation and infection, while fungi and yeasts remain understudied. The aim of this study was to analyse the mycobiota and its interactions with the bacterial microbiota in light ofC. difficilecolonisation and infection.MethodsThe mycobiota was profiled by ITS2 sequencing of faecal DNA from infected patients (CDI; n = 29), asymptomatically colonised patients (CDC; n = 38) and hospitalised controls withC. difficilenegative stool culture (Controls; n = 38). Previously published 16S rRNA gene sequencing data of the same cohort were used additionally for machine learning and fungal-bacterial network analysis.ResultsCDI patients were characterised by a significantly higher abundance ofCandidaspp. (MD 0.270 ± 0.089,P= 0.002) andCandida albicans(MD 0.165 ± 0.082,P= 0.023) compared to Controls. Additionally, they were deprived ofAspergillusspp. (MD -0.067 ± 0.026,P= 0.000) andPenicilliumspp. (MD -0.118 ± 0.043,P= 0.000) compared to CDC patients. Network analysis revealed a positive association between several fungi and bacteria in CDI and CDC, although the analysis did not reveal a direct association betweenClostridioidesspp. and fungi. Furthermore, the microbiota machine learning model outperformed the models based on the mycobiota and the joint microbiota-mycobiota model. The microbiota classifier successfully distinguished CDI from CDC (AUROC = 0.884) and CDI from Controls (AUROC = 0.905).BlautiaandBifidobacteriumwere marker genera associated with CDC patients and Controls.ConclusionsThe gut mycobiota differs between CDI, CDC, and Controls, and may affectClostridioidesspp. through indirect interactions. The identification of bacterial marker genera associated with CDC and Controls warrants further investigation. Although the mycobiota’s predictive value ofC. difficilestatus was low, fungal-bacterial interactions might be considered when diagnosing and treatingC. difficileinfection.
The Septin Cytoskeleton is Required for Plasma Membrane Repair
Authors: Prislusky M. Isabella , Lam Jonathan GT , Contreras Viviana Ruiz , Ng Marilynn , Chamberlain Madeline , Pathak-Sharma Sarika , Fields Madalyn , Zhang Xiaoli , Amer Amal O. , Seveau Stephanie 
Published: July 2023

ABSTRACTMammalian cells are frequently exposed to mechanical and biochemical stressors resulting in plasma membrane injuries. Repair mechanisms reseal the plasma membrane to restore homeostasis and prevent cell death. In the present work, a silencing RNA screen was performed to uncover plasma membrane repair mechanisms of cells exposed to a pore-forming toxin (listeriolysin O). This screen identified molecules previously known to repair the injured plasma membrane such as annexin A2 (ANXA2) as well as novel plasma membrane repair candidate proteins. Of the novel candidates, we focused on septin 7 (SEPT7) because the septins are an important family of conserved eukaryotic cytoskeletal proteins. Using diverse experimental approaches, we established for the first time that SEPT7 plays a general role in plasma membrane repair of cells perforated by pore-forming toxins and mechanical wounding. Remarkably, upon cell injury, the septin cytoskeleton is extensively redistributed in a Ca2+-dependent fashion, a hallmark of plasma membrane repair machineries. The septins reorganize into subplasmalemmal domains arranged as knob and loop (or ring) structures containing F-actin, myosin II, and annexin A2 (ANXA2) and protrude from the cell surface. Importantly, the formation of these domains correlates with the plasma membrane repair efficiency. Super-resolution microscopy shows that septins and actin are arranged in intertwined filaments associated with ANXA2. Silencing SEPT7 expression prevented the formation of the F-actin/myosin II/ANXA2 domains, however, silencing expression of ANXA2 had no observable effect on their formation. These results highlight the key structural role of the septins in remodeling the plasma membrane and in the recruitment of the repair molecule ANXA2. Collectively, our data support a novel model in which the septin cytoskeleton acts as a scaffold to promote the formation of plasma membrane repair domains containing contractile F-actin and annexin A2.
Occurrence of strawberry viruses inFragariagermplasm and evaluation of cryotherapy as an eradication method for strawberry viruses
Authors: Wöhner Thomas , Höfer Monika 
Published: July 2023

AbstractStrawberry plants are highly susceptible to viral infections, which pose significant threats to global strawberry production. This study aims to explore the efficacy ofin vitroinitiation and cryopreservation of shoot tips as a potential strategy for eradicating strawberry viruses. We tested plants for four important strawberry viruses namely: SMoV, SCV, SMEY and SVBV. The plants, which tested positive were either cultivated as in vitro cultures then returned to a green house or field collection cultivation, or treated by cryopreservation. After cryopreservation, the plants were cultivated again in vitro and then in the green house or field. The viruses were detected within each propagation step. Significant eradication effects were found for SMoV and SCV when plants were treated byin vitroinitiation or with cryotherapy, but not for SMEY or SVBV. The results of this study show that cryotherapy orin vitroinitiation can lead to the elimination of strawberry viruses, but the kind of therapy appears to depend on the type of virus.
Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite- oxidizing strains
Authors: Kolovou Maria , Panagiotou Dimitra , Süße Lars , Loiseleur Olivier , Williams Simon , Karpouzas Dimitrios G. , Papadopoulou Evangelia S. 
Published: July 2023

AbstractNitrification is associated with significant losses of fertilizer-derived ammonium from agroecosystems. The use of biological nitrification inhibitors (BNIs), in place of synthetic nitrification inhibitors (SNIs), holds a great potential to effectively reduce N losses and conforms with the current move towards ecological-intensified agriculture. Knowledge of the activity of BNIs to soil nitrifiers is limited and is mostly based on bioassays with a singleNitrosomonas europaeastrain. We determined thein vitroactivity of multiple plant-derived compounds as BNIs like (i) root-derived compounds (sakuranetin, MHPP, and zeanone); (ii) other phytochemicals (caffeic acid, quinic acid, chlorogenic acid and shikimic acid), and (iii) analogues of statins (simvastatin), triazoles (1-butyl-4-propyl-triazole, 1,4-dibutyltriazole) and zeanone (2-methoxy-1,4-naphthoquinone), on ecophysiologically and phylogenetically distinct soil-derived ammonia-oxidizing bacteria (AOB) (Nitrosospira multiformisandN. europaea), ammonia-oxidizing archaea (AOA) (CandidatusNitrosotalea sinensis andCandidatusNitrosocosmicus franklandianus), and a nitrite-oxidizing bacterium (NOB) (Nitrobactersp. NHB1). AOA were more sensitive than AOB to BNIs. Sensitivity within AOA group was BNI-dependent, unlike AOB for whichN. multiformiswas consistently more sensitive thanN. europaea. Interestingly, several compounds were inhibitory toNitrobactersp. with MHPP and caffeic acid being more potent to the NOB compared to the AOB and AOA strains, an observation with potentially serious implications for soil quality and agricultural production. Overall, zeanone, MHPP and caffeic acid were the most potent ΒNIs towards AOB, zeanone and 2-methoxy-1,4-naphthoquinone were the most effective compounds against AOA, while caffeic acid was the most potent BNI onNitrobactersp. We provide pioneering evidence for the activity range of multiple BNIs on soil nitrifiers, stress the need for revisiting the biological screening systems currently used for BNI determination and we sought for a more thorough monitoring of the impact of BNI candidates on a range of both target and non-target microorganisms.