bluuebunny/crossref_metadata_2025 huggingface dataset:
Hostile attribution bias shapes neural synchrony in the left ventromedial prefrontal cortex during ambiguous social narratives
Authors: Lyu Yizhou , Su Zishan , Neumann Dawn , Meidenbauer Kimberly L. , Leong Yuan Chang
Published: July 2023

Hostile attribution bias refers to the tendency to interpret social situations as intentionally hostile. While previous research has focused on its developmental origins and behavioral consequences, the underlying neural mechanisms remain underexplored. Here, we employed functional near infrared spectroscopy (fNIRS) to investigate the neural correlates of hostile attribution bias. While undergoing fNIRS, participants listened to and provided attribution ratings for 21 hypothetical scenarios where a character’s actions resulted in a negative outcome for the listener. Ratings of hostile intentions were averaged to obtain a measure of hostile attribution bias. Using intersubject-representational similarity analysis, we found that participants with similar levels of hostile attribution bias exhibited higher levels of neural synchrony during narrative listening, suggesting shared interpretations of the scenarios. This effect was localized to the left ventromedial prefrontal cortex (VMPFC), and was particularly prominent in scenarios where the character’s intentions were highly ambiguous. We then grouped participants into high and low bias groups based on a median split of their hostile attribution bias scores. A similarity-based classifier trained on the neural data classified participants as having high or low bias with 76% accuracy, indicating that the neural time courses during narrative listening was systematically different between the two groups. Furthermore, hostile attribution bias correlated negatively with attributional complexity, a measure of one’s tendency to consider multifaceted causes when explaining behavior. Our study sheds light on the neural mechanisms underlying hostile attribution bias and highlights the potential of using fNIRS to develop non-intrusive and cost-effective neural markers of this socio-cognitive bias.

Significance Statement

Inferring the intentions from behavior is crucial for adaptive social functioning. A predisposition towards interpreting intentions as hostile is a significant predictor of interpersonal conflict and aggressive tendencies. Using fNIRS, we found that individual differences in hostile attribution bias shaped neural synchrony in the VMPFC while processing real-world social situations. Additionally, we were able to distinguish between participants with high and low hostile attribution bias from neural activity time courses. These results reveal how subjective interpretations of social situations are influenced by hostile attribution bias and reflected in the temporal dynamics of the VMPFC. Our findings lay the groundwork for future studies aimed at understanding the neurobiological basis of socio-cognitive biases, as well as interventions aimed at mitigating these biases.
MARK2 phosphorylates KIF13A at a 14-3-3 binding site to polarize vesicular transport of transferrin receptor within dendrites
Authors: Han Yue , Li Min , Zhao Bingqing , Wang Huichao , Liu Yan , Liu Zhijun , Xu Jiaxi , Yang Rui
Published: July 2023

Neurons regulate the microtubule-based transport of certain vesicles selectively into axons or dendrites to ensure proper polarization of function. The mechanism of this polarized vesicle transport is still not fully elucidated, though it is known to involve kinesins, which drive anterograde transport on microtubules. Here we explore how the kinesin-3 family member KIF13A is regulated such that vesicles containing transferrin receptor (TfR) travel only to dendrites. In experiments involving live-cell imaging, knockout of KIF13A, BioID assay, we found that the kinase MARK2 phosphorylates KIF13A at a 14-3-3 binding motif, strengthening interaction of KIF13A with 14-3-3 such that it dissociates from TfR-containing vesicles, which therefore cannot enter axons. Overexpression of KIF13A or knockout of MARK2 leads to axonal transport of TfR-containing vesicles. These results suggest a novel kinesin-based mechanism for polarized transport of vesicles to dendrites.

Significance

Our findings suggest that at least one type of vesicles, those containing transferrin receptor, travel exclusively to dendrites and are excluded from axons because the kinase MARK2 phosphorylates the kinesin KIF13A to promote its separation from vesicles at the proximal axon, preventing vesicle transport into axons, such that they travel only to dendrites. Future studies should explore how this mechanism of polarized vesicle transport supports neuronal function.
Identifying Selectivity Filters in Protein Biosensor for Ligand Screening
Authors: Sahil Mohammad , Singh Jayanti , Sahu Subhankar , Pal Sushant , Yadav Ajit , Anand Ruchi , Mondal Jagannath
Published: July 2023

Specialized sensing mechanisms in bacteria enable the identification of cognate ligands with remarkable selectivity in highly xenobiotic-polluted environments, where these ligands are utilized as energy sources. Here, via an integrated all-atom computer simulation, biochemical assay and isothermal titration calorimetry approaches we determine the molecular basis of MopR, a phenol biosensor’s complex selection process of ligand entry. Our results reveal a set of strategically placed selectivity filters along the ligand entry pathway of MopR. These filters act as checkpoints, screening diverse aromatic ligands at the protein surface based on their chemical features and sizes. Ligands meeting specific criteria are allowed to enter the sensing site in an orientation-dependent manner. Sequence and structural analyses demonstrate the conservation of this ligand entry mechanism across the sensor class, with individual amino acids along the selectivity filter path playing a critical role in ligand selection. Together, this investigation highlights the importance of interactions with the ligand entry pathway, in addition to interactions within the binding pocket, for achieving ligand selectivity in biological sensing. The findings enhance our understanding of ligand selectivity in bacterial phenol biosensors and provide insights for the rational expansion of the biosensor repertoire, particularly for the biotechnologically relevant class of aromatic pollutants.
An interpretable deep learning framework for genome-informed precision oncology
Authors: Ren Shuangxia , Cooper Gregory F , Chen Lujia , Lu Xinghua
Published: July 2023

Cancers result from aberrations in cellular signaling systems, typically resulting from driver somatic genome alterations (SGAs) in individual tumors. Precision oncology requires understanding the cellular state and selecting medications that induce vulnerability in cancer cells under such conditions. To this end, we developed a computational framework consisting of two components: 1) A representation-learning component, which learns a representation of the cellular signaling systems when perturbed by SGAs, using a biologically-motivated and interpretable deep learning model. 2) A drug-response-prediction component, which predicts the response to drugs by leveraging the information of the cellular state of the cancer cells derived by the first component. Our cell-state-oriented framework significantly enhances the accuracy of genome-informed prediction of drug responses in comparison to models that directly use SGAs as inputs. Importantly, our framework enables the prediction of response to chemotherapy agents based on SGAs, thus expanding genome-informed precision oncology beyond molecularly targeted drugs.
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

Correlative 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

Non-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

Insects 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

Background

Dysregulated 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.

Methods

Participants 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.

Results

In 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.

Conclusions

Consistent 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

MYCN 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

Purpose

Postoperative 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.

Methods

A 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.

Results

Ninety-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.

Conclusions

We 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

Existing 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

Like 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

Objectives

The 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.

Methods

The 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.

Results

CDI 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.

Conclusions

The 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

Mammalian 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

Strawberry 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

Nitrification 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.
3D osteocyte lacunar morphometry of human bone biopsies with high resolution microCT: from monoclonal gammopathy to newly diagnosed multiple myeloma
Authors: Moreno-Jiménez Inés , Heinig Sharen , Heras Unai , Maichl Daniela Simone , Strifler Susanne , Leich Ellen , Blouin Stéphane , Fratzl Peter , Fratzl-Zelman Nadja , Jundt Franziska , Cipitria Amaia
Published: July 2023

Osteocytes are mechanosensitive, bone-embedded cells which are connected via dendrites in a lacuno-canalicular network and regulate bone resorption and formation balance. Alterations in osteocyte lacunar volume, shape and density have been identified in conditions of aging, osteoporosis and osteolytic bone metastasis, indicating patterns of impaired bone remodeling, osteolysis and disease progression. Osteolytic bone disease is a hallmark of the hematologic malignancy multiple myeloma (MM), in which monoclonal plasma cells in the bone marrow disrupt the bone homeostasis and induce excessive resorption at local and distant sites. Qualitative and quantitative changes in the 3D osteocyte lacunar morphometry have not yet been evaluated in MM, nor in the precursor conditions monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). In this study, we characterized the osteocyte lacunar morphology in trabecular bone of the iliac crest at the ultrastructural level using high resolution microCT in human bone biopsy samples of three MGUS, two SMM and six newly diagnosed MM. In MGUS, SMM and MM we found a trend for lower lacunar density and a shift towards larger lacunae with disease progression (higher 50% cutoff of the lacunar volume cumulative distribution) in the small osteocyte lacunae 20-900 μm3range compared to control samples. In the larger lacunae 900-3000 μm3range, we detected significantly higher lacunar density and microporosity in the MM group compared to the MGUS/SMM group. Regarding the shape distribution, the MGUS/SMM group showed a trend for flatter, more elongated and anisotropic osteocyte lacunae compared to the control group. Altogether, our findings suggest that osteocytes in human MM bone disease undergo changes in their lacunae density, volume and shape, which could be an indicator for osteolysis and disease progression. Future studies are needed to understand whether alterations of the lacunae architecture affect the mechanoresponsiveness of osteocytes and ultimately bone adaptation and fracture resistance in MM and its precursors conditions.
Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images
Authors: Daviet Benoit , Fournier Christian , Cabrera-Bosquet Llorenç , Simonneau Thierry , Cafier Maxence , Romieu Charles
Published: July 2023

Background

Grapevine berries undergo asynchronous growth and ripening dynamics within the same bunch. Due to the lack of efficient methods to perform sequential non-destructive measurements on a representative number of individual berries, the genetic and environmental origins of this heterogeneity, as well as its impacts on both vine yield and wine quality, remain nearly unknown. To address these limitations, we propose to track the growth and coloration kinetics of individual berries on time-lapse images of grapevine bunches.

Result

First, a deep-learning approach is used to detect berries with at least 50±10% of visible contours, and infer the shape they would have in the absence of occlusions. Second, a tracking algorithm was developed to assign a common label to shapes representing the same berry along the time-series. Training and validation of the methods were performed on challenging image datasets acquired in a robotised high-throughput phenotyping platform. Berries were detected on various genotypes with a F1-score of 91.8%, and segmented with a mean absolute error of 4.1% on their area. Tracking allowed to label and retrieve the temporal identity of more than half of the segmented berries, with an accuracy of 98.1%. This method was used to extract individual growth and colour kinetics of various berries from the same bunch, allowing us to propose the first statistically relevant analysis of berry ripening kinetics, with a time resolution lower than one day.

Conclusions

We successfully developed a fully-automated open-source method to detect, segment and track overlapping berries in time-series of grapevine bunch images. This makes it possible to quantify fine aspects of individual berry development, and to characterise the asynchrony within the bunch. The interest of such analysis was illustrated here for one genotype, but the method has the potential to be applied in a high throughput phenotyping context. This opens the way for revisiting the genetic and environmental variations of the ripening dynamics. Such variations could be considered both from the point of view of fruit development and the phenological structure of the population, which would constitute a paradigm shift.
Single-molecule digital sizing of proteins in solution
Authors: Krainer Georg , Jacquat Raphael P.B. , Schneider Matthias M. , Welsh Timothy J. , Fan Jieyuan , Peter Quentin A. E. , Andrzejewska Ewa A. , Šneiderienė Greta , Czekalska Magdalena A. , Ausserwoeger Hannes , Chai Lin , Arter William E. , Saar Kadi L. , Herling Therese W. , Franzmann Titus M. , Kosmoliaptsis Vasilis , Alberti Simon , Hartl F.-Ulrich , Lee Steven F. , Knowles Tuomas P.J.
Published: July 2023

Proteins constitute the molecular machinery of life and exert their biological function by interacting with other proteins, as well as by assembling into biomolecular complexes and higher order structures. Characterizing the sizes, interactions, and assembly states of proteins is thus key for understanding the normal functional behavior of proteins and for elucidating aberrant processes and interactions that can lead to dysfunction and disease. However, the physical characterization of proteins has remained a challenging problem due to the inherent compositional heterogeneity of protein mixtures as well as the polydisperse nature of protein complexes. Here, we address this challenge by demonstrating measurements of molecular diffusivity of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. The approach, termed single-molecule microfluidic diffusional sizing (smMDS), allows individual molecules to be counted directly, that is, in a digital manner, to enable calibration-free single-molecule diffusional-sizing-based monitoring of protein hydrodynamic radii even within heterogenous multicomponent mixtures. Applying smMDS to a variety of protein systems, we show that the high sensitivity provided by smMDS enables ultrasensitive sizing of proteins down to the femtomolar concentration range. We further demonstrate the applicability of the approach towards affinity profiling of protein interactions at the single-molecule level and illustrate the potential of smMDS in resolving different assembly states of high- and low-molecular weight protein oligomers. Furthermore, we highlight the digital nature of the detection process by sizing multiple protein species within complex aggregation mixtures. Finally, we apply the approach to characterize nanoscale clusters of a phase separating protein system. Taken together, smMDS constitutes a versatile approach for digital, in-solution characterization of the sizes, interactions, and assembly states of proteins. We anticipate that smMDS will facilitate the discovery of new biomolecular mechanisms of proteins and will find broad applicability in the analysis of protein complexes in the biological, biophysical, and biomedical sciences, and beyond.
Mechanisms of Innate Immune Injury in Arrhythmogenic Cardiomyopathy
Authors: Chelko Stephen P. , Penna Vinay , Engel Morgan , Landim-Vieira Maicon , Cannon Elisa N. , Lavine Kory , Saffitz Jeffrey E.
Published: July 2023

Inhibition of nuclear factor kappa-B (NFκB) signaling prevents disease inDsg2mut/mutmice, a model of arrhythmogenic cardiomyopathy (ACM). Moreover, NFκB is activated in ACM patient-derived iPSC-cardiac myocytes under basal conditionsin vitro. Here, we used genetic approaches and sequencing studies to define the relative pathogenic roles of immune signaling in cardiac myocytes vs. inflammatory cells inDsg2mut/mutmice. We found that NFκB signaling in cardiac myocytes drives myocardial injury, contractile dysfunction, and arrhythmias inDsg2mut/mutmice. It does this by mobilizing cells expressing C-C motif chemokine receptor-2 (CCR2+ cells) to the heart, where they mediate myocardial injury and arrhythmias. Contractile dysfunction inDsg2mut/mutmice is caused both by loss of heart muscle and negative inotropic effects of inflammation in viable muscle. Single nucleus RNA sequencing and cellular indexing of transcriptomes and epitomes (CITE-seq) studies revealed marked pro-inflammatory changes in gene expression and the cellular landscape in hearts ofDsg2mut/mutmice involving cardiac myocytes, fibroblasts and CCR2+ cells. Changes in gene expression in cardiac myocytes and fibroblasts inDsg2mut/mutmice were modulated by actions of CCR2+ cells. These results highlight complex mechanisms of immune injury and regulatory crosstalk between cardiac myocytes, inflammatory cells, and fibroblasts in the pathogenesis of ACM.

BRIEF SUMMARY

We have uncovered a therapeutically targetable innate immune mechanism regulating myocardial injury and cardiac function in a clinically relevant mouse model of Arrhythmogenic Cardiomyopathy (ACM).
PP2A inhibition instructs spliceosome phosphorylation to create splicing vulnerability in colon adenocarcinoma
Authors: Dias Matheus H. , Liudkovska Vladyslava , Bleijerveld Onno B. , Velds Arno , Bernards René , Cieśla Maciej
Published: July 2023

Protein phosphatase 2A (PP2A) is a versatile enzyme affecting many aspects of cellular physiology. However, it remains unclear which of the cellular processes are most perturbed upon PP2A inhibition and how these perturbations could be exploited therapeutically. We report an unanticipated sensitivity of the splicing machinery to phosphorylation changes in response to PP2A inhibition by LB-100 in colorectal adenocarcinoma. We observe enrichment for differentially phosphorylated sites within cancer-critical splicing nodes of U2 snRNP, SRSF and hnRNP proteins. Altered phosphorylation endows LB-100-treated colorectal adenocarcinoma cells with differential splicing patterns. In PP2A-inhibited cells, over 1000 events of exon skipping and intron retention affect regulators of genomic integrity. Finally, LB-100-evoked alternative splicing is predicted to be a source of neoantigens that can improve cancer treatment responses to immune modulators. Our findings provide a potential explanation for the pre-clinical and clinical observations that PP2A inhibition sensitizes cancer cells to immune checkpoint blockade and genotoxic agents.
BNIP3-mediated mitophagy boosts the competitive dominant growth of lenvatinib resistant cells via reprogramming energy metabolism in HCC
Authors: Wang Sikai , Cheng Hongxia , Li Miaomiao , Wu Haoran , Zhang Shanshan , Gao Dongmei , Huang Yilan , Guo Kun
Published: July 2023

Although increasing studies has demonstrated that cell competition widely involved in the growth and homeostasis of multicellular organisms is closely linked to tumorigenesis and development, the mechanistic contributions to the association between tumor cell competition-driven heterogeneity and drug resistance remains ill-defined. In our study, lenvitinib-resistant hepatocellular carcinoma (HCC) cells display obviously competitive growth dominance against sensitive cells through reprogramming energy metabolism. Mechanistically, when BCL2 interacting protein3 (BNIP3) overexpression activates mitophagy activity in lenvatinib-resistant HCC cells, energy imbalance signal caused by reduced mitochondrial oxidative phosphorylation levels provokes the phosphorylation of AMP-activated protein kinase (AMPK) sensor; subsequently, enabled AMPK specifically targets enolase 2 (ENO2) to enhance glycolysis and eventually promots the competitive capacity and dominant growth. Of note, BNIP3 deficiency shows certain inhibition of cell competition outcome. Our findings emphasize a vital role for BNIP3-AMPK-ENO2 signaling in maintaining the competitive outcome of lenvitinib-resistant HCC cells via regulating energy metabolism; meanwhile this work recognaizes BNIP3 as a promising target to overcome HCC drug resistance.
Teosinte Pollen Driveguides maize diversification and domestication by RNAi
Authors: Berube Benjamin , Ernst Evan , Cahn Jonathan , Roche Benjamin , Alves Cristiane de Santis , Lynn Jason , Scheben Armin , Siepel Adam , Ross-Ibarra Jeffrey , Kermicle Jerry , Martienssen Rob
Published: July 2023

Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describeTeosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosintemexicana(Zea mays ssp. mexicana), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin inmexicanadepend onDicer-Like 2 (Dcl2)and targetTeosinte Drive Responder 1 (Tdr1),which encodes a lipase required for pollen viability.Dcl2,Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression ofmexicanainto early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion inmexicanaspans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosintemexicanareveals correlated patterns of admixture among unlinked genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids.Teosinte Pollen Drivelikely played a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of “self” small RNAs in the germlines of plants and animals.
Modular and integrative activity reporters enhance biochemical studies in the yeast ER
Authors: Martinusen Samantha G , Slaton Ethan W , Nelson Sage E , Pulgar Marian A , Besu Julia T , Simas Cassidy F , Denard Carl A
Published: July 2023

The yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.