bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and powdery mildew susceptibility
Authors: Huebbers Jan W. , Caldarescu George A. , Kubátová Zdeňka , Sabol Peter , Levecque Sophie C. J. , Kuhn Hannah , Kulich Ivan , Reinstädler Anja , Büttgen Kim , Manga-Robles Alba , Mélida Hugo , Pauly Markus , Panstruga Ralph , Žárský Viktor 
Published: December 2022

AbstractEXO70 proteins are essential constituents of the octameric exocyst complex implicated in vesicle tethering during exocytosis, while MLO proteins are plant-specific calcium channels of which some isoforms play a key role during fungal powdery mildew pathogenesis. We here detected by a variety of histochemical staining procedures an unexpected phenotypic overlap ofA. thaliana exo70H4andmlo2 mlo6 mlo12triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses of isolated trichomes corroborated deficiencies in the composition of trichome cell walls inexo70H4andmlo2 mlo6 mlo12mutants. Transgenic lines expressing fluorophore- tagged EXO70H4 and MLO variants exhibited extensive co-localization of these proteins at the trichome plasma membrane and cell wall. Furthermore, mCherry- EXO70H4 mislocalized in trichomes of themlotriple mutant and,vice versa, MLO6- GFP exhibited aberrant subcellular localization in trichomes of theexo70H4mutant. Transgenic expression of GFP-marked PMR4 callose synthase, a previously identified cargo of EXO70H4 dependent exocytosis, revealed reduced cell wall delivery of GFP- PMR4 inmlotriple mutant plants.In vivoprotein-protein interaction assays uncovered isoform-preferential physical interaction between EXO70 and MLO proteins. Finally,exo70H4andmlomutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform- specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility, possibly by (co-)regulating focal secretion of cell wall-related cargo.
A multi-omicNicotiana benthamianaresource for fundamental research and biotechnology
Authors: Ranawaka Buddhini , An Jiyuan , Lorenc Michał T. , Jung Hyungtaek , Sulli Maria , Aprea Giuseppe , Roden Sally , Hayashi Satomi , Cooper Tal , LeBlanc Zacharie , Llaca Victor , Orzaez Diego , Bombarely Aureliano , Bally Julia , Winefield Christopher , Giuliano Giovanni , Waterhouse Peter M. 
Published: December 2022

AbstractNicotiana benthamianais an invaluable model plant and biotechnology platform. To further improve its usefulness and versatility, we have produced high quality chromosome level genome assemblies and multi-omic datasets for both the ubiquitously used LAB strain and a distantly related wild accession, QLD, as well as mapping their single nucleotide polymorphisms with two additional laboratory and four additional wild accessions. LAB and QLD have many genetic, functional, and metabolic differences. These coupled with their high inter-fertility and equally efficient transient and stable transformation and genome editing provide a powerful resource partnership. Their ∼3Gb allotetraploid genomes show advanced diploidisation with major chromosome loss and rearrangement, extensive homoeologous gene loss, and widespread segmental allopolyploidy. Recent bursts of Copia mobility, not seen in otherNicotianagenomes, have probably aidedN. benthamiana’s adaptation to a spectrum of Australian ecologies.
Obtaining Increased Functional Proteomics Insights from Thermal Proteome Profiling through Optimized Melt Shift Calculation and Statistical Analysis
Authors: McCracken Neil A. , Liu Hao , Runnebohm Avery M. , Wijeratne H.R. Sagara , Wijeratne Aruna B. , Staschke Kirk A. , Mosley Amber L. 
Published: December 2022

ABSTRACTThermal Proteome Profiling (TPP) is an invaluable tool for functional proteomics studies that has been shown to discover changes associated with protein-ligand, protein- protein, and protein-RNA interaction dynamics along with changes in protein stability resulting from cellular signaling. The increasing number of reports employing this assay has not been met concomitantly with advancements and improvements in the quality and sensitivity of the corresponding data analysis. The gap between data acquisition and data analysis tools is even more apparent as TPP findings have reported more subtle melt shift changes related to protein post-translational modifications. In this study, we have improved the Inflect data analysis pipeline (now referred to as InflectSSP, available athttps://CRAN.R-project.org/package=InflectSSP) to increase the sensitivity of detection for both large and subtle changes in the proteome as measured by TPP. Specifically, InflectSSP now has integrated statistical and bioinformatic functions to improve objective functional proteomics findings from the quantitative results obtained from TPP studies through increasing both the sensitivity and specificity of the data analysis pipeline. To benchmark InflectSSP, we have reanalyzed two publicly available datasets to demonstrate the performance of this publicly available R based program for TPP data analysis. Additionally, we report new findings following temporal treatment of human cells with the small molecule Thapsigargin which induces the unfolded protein response (UPR). InflectSSP analysis of our UPR study revealed highly reproducible target engagement over time while simultaneously providing new insights into the dynamics of UPR induction.
Enzyme encapsulation peptides bind to the groove between tessellating subunits of the bacterial microcompartment shell
Authors: Bradley-Clarke Jack , Gu Shuang , Rose Ruth-Sarah , Warren Martin J. , Pickersgill Richard W. 
Published: December 2022

AbstractBacterial microcompartments are prokaryotic organelles consisting of encapsulated enzymes within a thin protein shell. They are involved in metabolic processing including propanediol, choline, glycerol and ethanolamine utilization, and carbon fixation. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the binding-site has not been revealed. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating tiles of major shell proteins.In silicodocking studies provide a compelling model of peptide binding to this hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell proteins faces the lumen of the microcompartment. Binding between shell protein tiles explains why the encapsulation peptide binding site has been elusive, how encapsulation-peptide bearing enzymes can promote shell assembly, and how the presence of cargo affects the size and shape of the bacterial microcompartment.
Neural populations in the language network differ in the size of their temporal receptive windows
Authors: Regev Tamar I. , Casto Colton , Hosseini Eghbal A. , Adamek Markus , Ritaccio Anthony L. , Willie Jon T. , Brunner Peter , Fedorenko Evelina 
Published: December 2022

AbstractDespite long knowing what brain areas support language comprehension, our knowledge of the neural computations that these frontal and temporal regions implement remains limited. One important unresolved question concerns functional differences among the neural populations that comprise the language network. Leveraging the high spatiotemporal resolution of intracranial recordings, we examined responses to sentences and linguistically degraded conditions and discovered three response profiles that differ in their temporal dynamics. These profiles appear to reflect different temporal receptive windows (TRWs), with average TRWs of about 1, 4, and 6 words, as estimated with a simple one-parameter model. Neural populations exhibiting these profiles are interleaved across the language network, which suggests that all language regions have direct access to distinct, multi-scale representations of linguistic input—a property that may be critical for the efficiency and robustness of language processing.
Transcriptional control of visual neural circuit development by GS homeobox 1
Authors: Schmidt Alexandra Rose , Shephard Rebekah , Patrick Regina L , Bergeron Sadie A 
Published: December 2022

ABSTRACTAs essential components of gene expression networks, transcription factors regulate neural circuit assembly.GS homeobox 1 (gsx1) is expressed in the developing visual system; however, no studies have examined its role in visual system formation. In zebrafish, retinal ganglion cell (RGC) axons terminate in ten arborization fields (AFs) in the optic tectum (TeO) and pretectum (Pr). Pretectal AFs (AF1-AF9) mediate distinct and essential visual behaviors, yet we understand less about their development compared to AF10 in the TeO. Usinggsx1zebrafish mutants, immunohistochemistry, and transgenic lines, we observed thatgsx1is required for vesicular glutamate transporter,slc17a6b, expression in the Pr, but not overall neuron number.gsx1mutants have normal eye morphology, yet exhibit impaired vision and a significantly reduced volume of RGC axons innervating the Pr and TeO, including loss of AF7. Consistent with this, prey capture is reduced ingsx1mutants. Timed laser ablation ofslc17a6b-positiveneurons reveals that they aide directly in AF7 formation. This work is the first to implicategsx1in establishing cell identity and functional neural circuits in the visual system.SUMMARY STATEMENTThis is the first study in any vertebrate model to establish a requirement for the homeobox transcription factor encoding gene,gsx1, in visual neural circuit formation and function.
CLIP-Seq Analysis Enables the Design of Ribosomal RNA Bait Oligonucleotides That Protect AgainstC9ORF72ALS/FTD-Associated Poly-GR Pathophysiology
Authors: Ortega Juan A. , Sasselli Ivan R. , Boccitto Marco , Fleming Andrew C. , Fortuna Tyler R. , Li Yichen , Sato Kohei , Clemons Tristan D. , Daley Elizabeth L. , Nguyen Thao P. , Anderson Eric N. , Ichida Justin K. , Pandey Udai B. , Wolin Sandra , Stupp Samuel I. , Kiskinis Evangelos 
Published: December 2022

ABSTRACTAmyotrophic lateral sclerosis and frontotemporal dementia patients with a hexanucleotide repeat expansion inC9ORF72(C9-HRE) accumulate poly-GR and poly-PR aggregates. The pathogenicity of these arginine-rich dipeptide repeats (R-DPRs) is thought to be driven by their propensity to bind to low complexity domains of multivalent proteins. However, the ability of R-DPRs to bind native RNA and the significance of this interaction remains unclear. We used computational and experimental approaches to characterize the physicochemical properties of R-DPRs and their interaction with RNA. We find that poly-GR predominantly binds ribosomal RNA (rRNA) in cells and exhibits an interaction that is predicted to be energetically stronger than that for associated ribosomal proteins. Critically, modified rRNA “bait” oligonucleotides restore poly-GR-associated ribosomal deficits in cells and ameliorate poly-GR toxicity in patient neurons andDrosophilamodels. Our work strengthens the hypothesis that ribosomal function is impaired by R-DPRs, highlights a role for direct rRNA binding in mediating ribosomal disfunction, and presents a strategy for protecting against C9-HRE pathophysiological mechanisms.
European Beech Spring Phenological Phase Prediction with UAV-derived Multispectral Indices and Machine Learning Regression
Authors: Krause Stuart , Sanders Tanja G.M. 
Published: December 2022

AbstractThe acquisition of phenological events play an integral part in investigating the effects of climate change on forest dynamics and assessing the potential risk involved with the early onset of young leaves. Large scale mapping of forest phenological timing using earth observation data, could facilitate a better understanding of phenological processes due to an added spatial component. The translation of traditional phenological ground observation data into reliable ground truthing for the purpose of the training and validation of Earth Observation (EO) mapping applications is a challenge. In this study, we explored the possibility of predicting high resolution phenological phase data for European beech (Fagus sylvatica) with the use of Unmanned Aerial Vehicle (UAV)-based multispectral indices and machine learning. Using a comprehensive feature selection process, we were able to identify the most effective sensors, vegetations indices, training data partitions, and machine learning models for phenological phase prediction. The best performing model that generalised well over various sites was the model utilising the Green Chromatic Coordinate (GCC) and Generalized Addictive Model (GAM) boosting. The GCC training data was derived from the radiometrically calibrated visual bands from a multispectral sensor and predicted using uncalibrated RGB sensor data. The final GCC/GAM boosting model was capable in predicting phenological phases on unseen datasets within a RMSE threshold of 0.5. This research shows the potential of the interoperability among common UAV-mounted sensors in particular the utility of readily available low cost RGB sensors. Considerable limitations were however discovered with indices implementing the near-infrared (NIR) band due to oversaturation. Future work involves adapting models to facilitate the ICP Forests phenological flushing stages.
Biphasic curvature-dependence of cell migration inside microcylinders: persistent randomness versus directionality
Authors: Yu Xiaoyu , Wang Haiqin , Ye Fangfu , Wang Xiaochen , Fan Qihui , Xinpeng Xu 
Published: December 2022

AbstractCell-scale curvature plays important roles in controlling cell and tissue behaviors. However, these roles have not been well quantified, and the underlying mechanisms remain elusive. We combine experiments with theory to study systematically the curvature-dependence of cell migration inside PDMS microcylinders. We find that persistence is positively correlated with speed, following the universal speed-persistence coupling relation,i.e., faster cells turn less. Cell migration inside microcylinders is anisotropic and depends on curvature in a biphasic manner. At small curvatures, as curvature increases, the average speed and anisotropy both increase, but surprisingly, the average persistence decreases. Whereas as the curvature increases over some threshold, cells detach from the surface, the average speed and anisotropy both decrease sharply but the average persistence increases. Moreover, interestingly, cells are found to leave paxillins along their trajectories (on curved but not planar surfaces), facilitating the assembly of focal adhesions of following cells. We propose a minimal model for the biphasic curvotaxis based on three mechanisms: the persistent random “noise”, the bending penalty of stress fibers, and the cell-surface adhesion. The findings provide a novel and general perspective on directed cell migration in the widely existing curved microenvironment of cellsin vivo.
Neuroendocrine control of catch-up growth in Drosophila
Authors: Vallejo Diana M , Saez Ernesto , García-López Lucia , Santoro Roberto , Dominguez Maria 
Published: December 2022

AbstractChildren and other vertebrate animals stunted due to malnutrition can compensate for this deficit by resuming growth at a higher-than-normal rate via a still ill-defined mechanism. High mortality and adverse effects later in life may offset the positive effects of catch-up growth. Here we report that the invertebrateDrosophila melanogasteralso experiences catch-up growth following a period of starvation, and the relaxin receptor Lgr4 instigates this catch-up growth. Starved larvae compensate for weight loss by growing two or more times faster and starting maturation within the same time as the non-starved sibling by preventing a rise in insulin-like growth (IGF)-induced ecdysone under Lgr4 control. Our data reveal that catch-up growth is associated with a surge of insulin, not IGF, which may clarify how catch-up growth often leads to metabolic problems and obesity.
Diversity and evolution of cerebellar folding in mammals
Authors: Heuer Katja , Traut Nicolas , de Sousa Alexandra A. , Valk Sofie , Toro Roberto 
Published: December 2022

AbstractThe process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. Ancestral estimations indicate that size and folding of the cerebrum and cerebellum increase and decrease concertedly through evolution. Our analyses confirm the strong correlation between cerebral and cerebellar volumes across species, and show that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial wavelength and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. These findings provide new insights into the diversity and evolution of cerebellar folding and its potential influence on brain organisation across species.
SAP30BP interacts with RBM17/SPF45 to promote splicing in a subset of human short introns
Authors: Fukumura Kazuhiro , Sperotto Luca , Seuß Stefanie , Kang Hyun-Seo , Yoshimoto Rei , Sattler Michael , Mayeda Akila 
Published: December 2022

SUMMARYHuman pre-mRNA splicing requires the removal of introns with highly variable lengths, from tens to over a million nucleotides. Therefore, mechanisms of intron recognition and splicing are likely not universal. Recently, we reported that splicing in a subset of human short introns with truncated polypyrimidine tracts depends on RBM17 (SPF45), instead of the canonical splicing factor U2AF heterodimer. Here, we demonstrate that SAP30BP, a factor previously implicated in transcriptional control, is an essential splicing cofactor for RBM17.In vitrobinding and NMR analyses demonstrate that a U2AF-homology motif (UHM) in RBM17 binds directly to a newly identified UHM-ligand motif (ULM) in SAP30BP. We show that this RBM17–SAP30BP interaction is required to specifically recruit RBM17 to phosphorylated SF3B1 (SF3b155), a U2 snRNP component in active spliceosomes. We propose a unique mechanism for splicing in a subset of short introns, in which SAP30BP guides RBM17 in the assembly of active spliceosomes.Graphical abstractIn briefFukumura et al. discover a general splicing mechanism in a subset of human short introns with truncated polypyrimidine tracts. This splicing reaction is mediated by intermediary RBM17–SAP30BP complex, instead of the known U2AF heterodimer. SAP30BP binding to RBM17 may support RBM17 association with active phosphorylated SF3B1 in U2 snRNP.HighlightsRBM17 (SPF45) is a splicing factor required for a subset of human short intronsSAP30BP is an essential cofactor, which interacts with RBM17viaUHM–ULM bindingRBM17 forms a weak complex with SAP30BP before its binding with SF3B1 in U2 snRNPRBM17–SAP30BP complex supports RBM17 to be recruited to active phosphorylated SF3B1
The development of object recognition requires experience with the surface features of objects
Authors: Wood Justin N. , Wood Samantha M. W. 
Published: December 2022

AbstractWhat role does visual experience play in the development of object recognition? Prior controlled-rearing studies suggest that newborn animals require slow and smooth visual experiences to develop object recognition. Here we examined whether the development of object recognition also requires experience with the surface features of objects. We raised newborn chicks in automated controlled-rearing chambers that contained a single virtual object, then tested their ability to recognize that object from familiar and novel viewpoints. When chicks were reared with an object that had surface features, the chicks developed view-invariant object recognition. In contrast, when chicks were reared with a line drawing of an object, the chicks failed to develop object recognition. The chicks reared with line drawings performed at chance level, despite acquiring over 100 hours of visual experience with the object. These results indicate that the development of object recognition requires experience with the surface features of objects.
The ketone body acetoacetate activates human neutrophils through FFA2R
Authors: Mårtensson Jonas , Björkman Lena , Lind Simon , Viklund Moa Bjerhem , Zhang Linjie , Gutierrez Saray , Dahlgren Claes , Sundqvist Martina , Xie Xin , Forsman Huamei 
Published: December 2022

AbstractNeutrophils express many surface receptors that sense environmental changes. One such sensor is FFA2R (free fatty acid receptor 2), a receptor that detects gut microbiota-derived short chain fatty acids. As such, FFA2R has been regarded as a molecular link between metabolism and inflammation. Our recent studies on FFA2R, using its endogenous agonist propionate in combination with allosteric modulators, have identified several novel aspects of FFA2R regulation. A recent study has also identified the ketone body acetoacetate as an endogenous ligand for mouse FFA2R. Whether human FFA2R also recognizes acetoacetate and how this recognition modulates human neutrophil functions has not been earlier investigated. In this study, we found that acetoacetate can induce a decrease of cAMP and translocation of β-arrestin in cells overexpressing FFAR2. In addition, we show that similar to propionate, FFA2R specific allosteric modulators enhance acetoacetate-induced transient rise in cytosolic calcium, production of reactive oxygen species and cell migration in human neutrophils. In summary, we demonstrate that human neutrophils recognize the ketone body acetoacetate through FFA2R. Thus, our data further highlight the key role of FFA2R in inflammation and metabolism.