bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the lipidome of Arabidopsis leaf mitochondria: Specific lipid complement and lipid biosynthesis capacity
Authors: Liu Yi-Tse , Senkler Jennifer , Herrfurth Cornelia , Braun Hans-Peter , Feussner Ivo 
Published: July 2022

SummaryMitochondria are often considered the power stations of the cell, playing critical roles in various biological processes such as cellular respiration, photosynthesis, stress responses and programmed cell death. To maintain the structural and functional integrities of mitochondria, it is crucial to achieve a defined membrane lipid composition between different lipid classes wherein specific proportions of individual lipid species are present. Although mitochondria are capable of self-synthesizing a few lipid classes, many phospholipids are synthesized in the endoplasmic reticulum and transferred to mitochondria via membrane contact sites, as mitochondria are excluded from the vesicular transportation pathway. However, knowledge on the capability of lipid biosynthesis in mitochondria and the precise mechanism of maintaining the homeostasis of mitochondrial lipids is still scarce. Here we describe the lipidome of mitochondria isolated fromArabidopsisleaves, including the molecular species of glycerolipids, sphingolipids and sterols to depict the lipid landscape of mitochondrial membranes. In addition, we define proteins involved in lipid metabolism by proteomic analysis and compare our data with mitochondria from cell cultures since they still serve as model system. Proteins putatively localized to the membrane contact sites are proposed based on the proteomic results and online databases. Collectively, our results suggest that leaf mitochondria are capable - with the assistance of membrane contact site-localised proteins - of generating several lipid classes including phosphatidylethanolamines, cardiolipins, diacylgalactosylglycerols and free sterols. We anticipate our work to be a foundation to further investigate the functional roles of lipids and their involvement in biochemical reactions in plant mitochondria.One sentence summaryThe lipid landscape of plant mitochondria suggests that they are capable in generating several phospholipid classes with the assistant of membrane contact site-localized proteins.
Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma
Authors: DeMartino Jeff , Meister Michael T. , Visser Lindy , Brok Mariël , Groot Koerkamp Marian J. A. , Hiemcke-Jiwa Laura S. , de Souza Terezinha , Merks Johannes H. M. , Holstege Frank C. P. , Margaritis Thanasis , Drost Jarno 
Published: July 2022

AbstractPaediatric rhabdomyosarcoma (RMS) is a soft tissue malignancy of mesenchymal origin which is thought to arise as a consequence of derailed myogenic differentiation. Despite intensive treatment regimens, the prognosis for high-risk patients remains dismal. The cellular differentiation states underlying RMS and how these relate to patient outcomes remain largely elusive. Here, we used single-cell mRNA-sequencing to generate a transcriptomic atlas of RMS. Analysis of the RMS tumour niche revealed evidence of an immunosuppressive microenvironment. We also identified an interaction between NECTIN3 and TIGIT, specific to the more aggressive fusion-positive (FP) RMS subtype, as a putative cause of tumour-induced T-cell dysfunction. In malignant RMS cells we defined transcriptional programs reflective of normal myogenic differentiation. Furthermore, we showed that these cellular differentiation states are predictive of patient outcomes in both FP RMS and the more clinically homogenous fusion-negative subtype. Our study reveals the potential of therapies targeting the immune microenvironment of RMS and suggests that assessing tumour differentiation states may enable a more refined risk stratification.
Hippocampal Place-like Signal in Latent Space
Authors: Schafer Matthew , Kamilar-Britt Philip , Sahani Vyoma , Bachi Keren , Schiller Daniela 
Published: July 2022

AbstractDuring navigation, the hippocampus represents physical places like coordinates on a map; similar location-like signals have been seen in sensory and concept spaces. It is unclear just how general this hippocampal place code is, however: does it map places in wholly non-perceivable spaces, without locations being instructed or reinforced and during navigation-like behavior? To search for such a signal, we imaged participants’ brains while they played a naturalistic, narrativebased social interaction game, and modeled their relationships as a kind of navigation through social space. Two independent samples showed hippocampal place-like signals in both region-based and whole-brain representational similarity analyses, as well as decoding and average pattern similarity analyses; the effects were not explained by other measures of the behavior or task information. These results are the first demonstration of complete domain generality in hippocampal place representation.One-Sentence Summaryhippocampal place-like signal in non-perceivable and unreinforced space during naturalistic navigational behavior.Significance statementThe hippocampus is a brain structure known to encode maps of physical spaces; this study shows that it also maps fully abstract, latent and uninstructed spaces. People played a naturalistic social interaction game while their brains were scanned. Hippocampal brain activity correlated with the fictional characters’ locations in an abstract social space framed by axes of affiliation and power, despite the participants never being exposed to a perceivable spatial representation. This mapping was present across multiple analyses and two samples, demonstrating that the brain system responsible for spatial mapping maps our social interactions too.
Dietary non-starch polysaccharides impair immunity to enteric nematode infection
Authors: Valente Angela H. , Jensen Karen M.R. , Myhill Laura J. , Zhu Ling , Mentzel Caroline M.J. , Krych Lukasz , Simonsen Henrik T. , Castro-Mejía Josue L. , Gobbi Alex , Bach Knudsen Knud Erik , Nielsen Dennis S. , Thamsborg Stig M. , Williams Andrew R. 
Published: July 2022

AbstractThe influence of diet on immune function and resistance to enteric infection and disease is becoming ever more established. Highly processed, refined diets can lead to inflammation and gut microbiome dysbiosis, whilst health-promoting dietary components such as phytonutrients and fermentable fibres are thought to promote a healthy microbiome and balanced mucosal immunity. Chicory (Cichorium intybus) is a leafy green vegetable rich in fibres and bioactive compounds that may promote gut health. Unexpectedly, we here show that incorporation of chicory into semisynthetic AIN93G diets renders mice susceptible to infection with enteric helminths. Mice fed a high level of chicory leaves (10% dry matter) had a more diverse gut microbiota, but a diminished type-2 immune response to infection with the intestinal roundworm Heligmosomoides polygyrus. Furthermore, the chicory-supplemented diet significantly increased burdens of the caecum-dwelling whipworm Trichuris muris, concomitant with a highly skewed type-1 immune environment in caecal tissue. The chicory-supplemented diet was rich in non-starch polysaccharides, particularly uronic acids (the monomeric constituents of pectin). In accordance, mice fed pectin-supplemented AIN93G diets had higher T. muris burdens and reduced IgE production and expression of genes involved in type-2 immunity. Importantly, treatment of pectin-fed mice with exogenous IL-25 restored type-2 responses and was sufficient to allow T. muris expulsion. Collectively, our data suggest that increasing levels of fermentable, non-starch polysaccharides in refined diets compromises immunity to helminth infection in mice. This diet-infection interaction may inform new strategies for manipulating the gut environment to promote resistance to enteric parasites.
Exploring DTI-derived metrics to non-invasively track recellularisation in vascular tissue engineering
Authors: Tornifoglio B , Stone A. J. , Mathieu P. , Fitzpatrick E. , Kerskens C. , Lally C. 
Published: July 2022

AbstractDespite significant growth in the field of tissue engineering over the past decades, non-invasive, non-destructive methods to characterise recellularisation of grafts are lacking. Here, we investigate a non-invasive magnetic resonance imaging technique, diffusion tensor imaging (DTI), within acellular and recellularised vascular grafts. Using two decellularised porcine carotid grafts, smooth muscle cells were cultured dynamically for two weeks with terminal time points at day 3, 7, and 14. Grafts were fixed at each time point and investigated by DTI in anex vivoset up. Semi-quantitative histology was carried out to investigate collagen, elastin, and cell density changes over time. DTI-derived metrics, namely the fractional anisotropy, mean diffusivity and tractography, not only were significantly different between day 3 and day 7 grafts, but also distinguished between acellular and recellularised grafts. Specifically, within the wet decellularised grafts, increasing fractional anisotropy was strongly correlated to increasing cell density. The results from this study show, for the first time, DTI’s place in the field of tissue engineering, offering non-invasive, non-destructive insight into graft recellularisation.
Diverse strategies for tracking seasonal environmental niches at hemispheric scale
Authors: Cohen Jeremy , Jetz Walter 
Published: July 2022

AbstractSpecies depend upon a constrained set of environmental conditions, or niches, for survival and reproduction that are increasingly lost under climatic change. Seasonal environments require species to either track their niches via movement or undergo physiological or behavioral changes to survive. Here we identify the tracking of both environmental niche position and breadth across 619 New World bird species and assess their phylogenetic and functional underpinning. Partitioning niche position and breadth tracking can inform whether climatic means or extremes limit seasonal distributions. We uncover diverse strategies, including the tracking of niche position, breadth, both, or neither, suggesting highly variable sensitivity to ongoing climatic change. There was limited phylogenetic determinism to this variation, but a strong association with functional attributes that differed between niche position and breadth tracking. Our findings imply significant functional consequences for communities and ecosystems as impending climate change affects some niche tracking strategies more than others.
Pollen accumulation on hawkmoths varies substantially among moth-pollinated flowers
Authors: Smith Gordon , Kim Christine , Raguso Robert 
Published: July 2022

AbstractUsing the pollen loads carried by floral visitors to infer their floral visitation behavior is a powerful technique to explore the foraging of wild pollinators. Interpreting these pollen records, however, requires assumptions about the underlying pollen dynamics. To compare visitor foraging across flower species, the most important assumption is that pollen is picked up and retained on the visitor at similar rates. Given differences in pollen presentation traits such as grain number or stickiness even among flowers with similar morphologies, however, the generality of this assumption is unclear. We investigated pollen accumulation on the hawkmoth Manduca sexta, testing the degree to which accumulation differed among flower species and how pollen stickiness affected this accumulation. In no-choice floral visitation assays to six plant species visited by long-tongued hawkmoths in the wild, M. sexta individuals were allowed to visit flowers 1, 2, or 5 times, after which the pollen on their proboscises was removed and counted. We found that the six plant species varied orders of magnitude in the number of pollen grains deposited on the moths, with some placing thousands of grains after a single visit and other placing none after five. Plant species with sticky pollen adhesion mechanisms placed more pollen on the moths and had relatively less pollen accumulation over successive visits than non-sticky plants. Intriguingly, moths carried fewer pollen grains after 5 visits than after 2 visits, suggesting that both sticky and non-sticky pollen was lost during foraging. Together, our results suggest that interpretation of pollen load data should be made cautiously, especially when comparing across plant species.
Choice-Induced Preference Change under a Sequential Sampling Model Framework
Authors: Lee Douglas G. , Pezzulo Giovanni 
Published: July 2022

AbstractSequential sampling models of choice, such as the drift-diffusion model (DDM), are frequently fit to empirical data to account for a variety of effects related to accuracy/consistency, response time (RT), and sometimes confidence. However, no model in this class can account for the phenomenon known aschoice-induced preference change, where decision makers tend to rate options higher after they choose them and lower after they reject them. Studies have reported choice-induced preference change for many decades, and the principal findings are robust. The resultingspreading of alternatives(SoA) in terms of their subjective value ratings is incompatible with traditional sequential sampling models, which consider the rated values of the options to be stationary throughout choice deliberation. Here, we propose an extension of the basic DDM that allows the drift rate to vary across deliberation time depending on which attributes are attended to at which points in time. Critically, the model assumes that choice deliberation commences based only on the more salient attributes of the options, and that additional attributes eventually come into consideration when the decision cannot be resolved based on the initial attributes alone. We show that this model can account for SoA (in addition to choice consistency and RT), as well as all previously reported relationships between SoA and choice difficulty, attribute disparity, and RT.
Mixed selectivity coding of content-temporal detail by dorsomedial posterior parietal neurons
Authors: Wang Lei , Zhou Xufeng , Zeng Fu , Cao Mingfeng , Zuo Shuzhen , Yang Jie , Kusunoki Makoto , Wang Huimin , Zhou Yong-di , Chen Aihua , Kwok Sze Chai 
Published: July 2022

SUMMARYThe dorsomedial posterior parietal cortex is part of a higher-cognition network implicated in elaborate processes underpinning memory formation, recollection, episodes reconstruction, and temporal information processing. Neural coding for complex episodic processing is however under-documented. Here we revealed a set of neural codes of ‘neuroethogram’ in the primate parietal cortex. Analyzing neural responses in macaque dmPPC to naturalistic videos, we discovered several groups of neurons that are sensitive to different categories of ethogram-items and to low-level sensory features, and saccadic eye movement. We also discovered that the processing of category and feature information by these neurons is sustained by accumulation of temporal information over a long timescale up to 30 s, corroborating its reported long temporal receptive windows. We performed an additional behavioral experiment and found that saccade-related activities could not account for the mixed neuronal responses elicited by the video stimuli. We further observed monkeys’ scan-paths and gaze consistency are modulated by video content. Taken altogether, these neural findings explain how dorsomedial PPC weaves fabrics of ongoing experiences together in real-time. The high dimensionality of neural representations should motivate us to shift the focus of attention from pure selectivity neurons to mixed selectivity neurons, especially in increasingly complex naturalistic task designs.HIGHLIGHTSNeural codes for “neuroethogram” in macaque dorsomedial parietal cortexParietal neural codes exhibit mixed selectivity of event featuresDorsomedial PPC neurons support a long temporal receptive window for episodesSaccadic movement could not explain away mixed neuronal responsesConsistency in scan-path and gaze shown across viewing repetitions
A Joint Distribution Approach on Non-linear Functional Connectivity
Authors: Yang Huzheng , Gu Shi 
Published: July 2022

AbstractThis report summarizes experiments on exploring non-linear functional connectivity. Using resting-state functional MRI data from the HCP1200 dataset, we define nodes as 17 functional networks and edges as the joint distribution between times series pairs. Linear dependence is removed before taking the joint distribution. We then employ a test for normality on the joint distribution to find non-normal distribution patterns. However, the result from an experimental run of 10 subjects shows that: only less than 1% of edges is non-normal distributed, and the location of such edges is not consistent across subjects. From this point of view, the non-linear part seems to be governed by random noise.
Translational regulation by RACK1 in astrocytes represses KIR4.1 expression and regulates neuronal activity
Authors: Oudart Marc , Avila-Gutierrez Katia , Moch Clara , Dossi Elena , Milior Giampaolo , Boulay Anne-Cécile , Gaudey Mathis , Moulard Julien , Lombard Bérangère , Loew Damarys , Bemelmans Alexis-Pierre , Rouach Nathalie , Chapat Clément , Cohen-Salmon Martine 
Published: July 2022

SummaryThe regulation of translation in astrocytes, the main glial cells in the brain, remains poorly characterized. We developed a high-throughput proteomic screen for polysome-associated proteins in astrocytes and focused on the ribosomal protein receptor of activated protein C kinase 1 (RACK1), a critical factor in translational regulation. In astrocyte somata and perisynaptic astrocytic processes (PAPs), RACK1 preferentially bound to a number of mRNAs, includingKcnj10, encoding the inward rectifying potassium (K+) channel KIR4.1, a critical astrocytic regulator of neurotransmission. By developing an astrocyte-specific, conditional RACK1 knock-out mouse model, we showed that RACK1 repressed the production of KIR4.1 in hippocampal astrocytes and PAPs. Reporter-based assays revealed that RACK1 controlledKcnj10translation through the transcript’s 5’ untranslated region. Upregulation of KIR4.1 in the absence of RACK1 modified the astrocyte territory volume and neuronal activity attenuatin burst frequency and duration in the hippocampus. Hence, astrocytic RACK1 represses KIR4.1 translation and influences neuronal activity.
Comparative Analysis of Commercially Available Typhoid Point of Care Tests: Results of a Prospective and Hybrid Retrospective Multicenter Diagnostic Accuracy Study in Kenya and Pakistan
Authors: Sapkota Jyotshna , Hasan Rumina , Onsare Robert , Arafah Sonia , Kariuki Sam , Shakoor Sadia , Qamar Farah , Mundalo Sheillah , Njeru Frida , Too Rael , Ndegwa Elizabeth , Andrews Jason R , Dittrich Sabine 
Published: July 2022

AbstractBlood and bone marrow cultures are considered the gold standard for the diagnosis of typhoid, but those methods require infrastructure and skilled manpower that are not always available in low- and middle-income countries where typhoid is endemic. The objective of the study is to evaluate the sensitivity and specificity of nine commercially available Salmonella Typhi rapid diagnostic tests (RDTs) using blood culture as reference standard in a multicenter study. This was a prospective and retrospective multicenter diagnostic accuracy study conducted in two geographically distant typhoid-endemic areas (Pakistan and Kenya; NCT04801602). 9 RDTs were evaluated were including Widal test. Point estimates for sensitivity and specificity were calculated using the Wilson method. Latent class analyses were performed using R to address the imperfect gold standard. 531 serum samples were evaluated (264 blood-culture positive; 267 blood-culture negative). The sensitivity of RDTs varied widely (range 0–78.8%), with the best overall performance shown by Enterocheck WB (72.7% sensitivity: 86.5% specificity). In latent class modeling, CTK IgG was found to have the highest sensitivity (79.1%), while the highest overall accuracy was observed with Enterocheck (73.8% sensitivity and 94.5% specificity). All commercially available Salmonella Typhi RDTs evaluated in the study had sensitivity and specificity values that fell below the required levels to be recommended for an accurate diagnosis. There were minimal differences in RDT performances between endemic regions. These findings highlight the clear need for new, more accurate Salmonella Typhi tests.
MAIT cells have a negative impact on glioblastoma
Authors: Keretsu Seketoulie , Hana Taijun , Lee Alexander , Kedei Noemi , Malik Nargis , Kim Hye , Spurgeon Jo , Khayrullina Guzal , Ruf Benjamin , Hara Ayaka , Coombs Morgan , Watowich Matthew , Hari Ananth , Ford Michael K.B. , Sahinalp Cenk , Watanabe Masashi , Zaki George , Gilbert Mark R. , Cimino Patrick. J. , Prins Robert , Terabe Masaki 
Published: July 2022

AbstractGlioblastoma (GBM) is the most aggressive primary brain cancer in adults and remains incurable. Our study revealed an immunosuppressive role of mucosal-associated invariant T (MAIT) cells in GBM. In bulk RNA sequencing data analysis of GBM tissues, MAIT cell gene signature significantly correlated with poor patient survival. A scRNA-seq of CD45+cells from 23 GBM tissue samples showed 15 (65.2%) were positive for MAIT cells and the enrichment of MAIT17. The MAIT cell signature significantly correlated with the activity of tumor-associated neutrophils (TANs) and myeloid-derived suppressor cells (MDSCs). Multiple immune suppressive genes known to be used by TANs/MDSCs were upregulated in MAIT-positive tumors. Spatial imaging analysis of GBM tissues showed that all specimens were positive for both MAIT cells and TANs and localized enrichment of TANs. These findings highlight the MAIT-TAN/MDSC axis as a novel therapeutic target to modulate GBM’s immunosuppressive tumor microenvironment.
The snapdragon genomes reveal the evolutionary dynamics of theSlocus supergene
Authors: Zhu Sihui , Zhang Yu’e , Copsy Lucy , Han Qianqian , Zheng Dongfeng , Coen Enrico , Xue Yongbiao 
Published: July 2022

AbstractThe multi-allelicS-locus, containing a pistilS-RNaseand dozens ofS-locus F-box (SLF), underlies genetic control of self-incompatibility (SI) inAntirrhinum hispanicum. The genusAntirrhinum, harboring such a SI system has been used as a model to study self-incompatibility extensively. However, there have been limited studies on the genomic organization of theS-locus supergene due to a lack of high-quality genomic data. Here, we present the chromosome-level reference and haplotype-resolved genome assemblies of a self-incompatibleAntirrhinum hispanicumline,AhS7S8. Alongside with the draft genome ofMisopates orontium, comparative genomics reveals thatA.hispanicumdiverged from its self-compatible cousin 12.3 million years ago (Mya). Expanded gene families enriched in distinct functional terms implied different evolutionary trajectories of outcrossing and selfing species. For the first time, two completeA.hispanicum S-haplotypes spanning ∼1.2Mb and containing 32SLFswere reconstructed, while most of theSLFsderived from retroelement-mediated proximal or tandem duplication approximately 122 Mya. Moreover, we detected a candidatecis-transcription factor associated with regulatingSLFs expression, and two miRNAs may control the expression of this transcription factor. Inter-specificS-locus and intra-specificS-haplotype comparisons revealed the dynamic nature and polymorphism of theS-locus supergene mediated by continuous gene duplication, segmental translocation or loss, and TE-involved transposition events. Our data provides an excellent resource for future research on the evolutionary studies onS-RNase-based self-incompatibility system.