bluuebunny/crossref_metadata_2025_split huggingface dataset:
FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT) interacts with OsIRO2 to regulate iron homeostasis
Authors: Liang Gang , Zhang Huimin , Li Yang , Pu Mengna , Yang Yujie , Li Chenyang , Lu Chengkai , Xu Peng , Yu Diqiu 
Published: March 2020

ABSTRACTThere are two Fe-uptake strategies for maintaining Fe homeostasis in plants. As a special graminaceous plant, rice applies both strategies. However, it remains unclear how these two strategies are regulated in rice. IRON-RELATED BHLH TRANSCRIPTION FACTOR 2 (OsIRO2) is critical for regulating Fe uptake in rice. In this study, we identified an interacting partner of OsIRO2,Oryza sativaFER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT), which encodes a bHLH transcription factor. The OsIRO2 protein is localized in the cytoplasm and nucleus, but OsFIT facilitates the accumulation of OsIRO2 in the nucleus. Loss-of-function mutations toOsFITresult in decreased Fe accumulation, severe Fe-deficiency symptoms, and disrupted expression of Fe-uptake genes. In contrast,OsFIToverexpression promotes Fe accumulation and the expression of Fe-uptake genes. Genetic analyses indicated thatOsFITandOsIRO2function in the same genetic node. Further analysis suggested that OsFIT and OsIRO2 form a functional transcription activation complex to initiate the expression of Fe-uptake genes. Our findings provide a mechanism understanding of how rice maintains Fe homeostasis.One-sentence summaryOsFIT interacts with and facilitates the accumulation of OsIRO2 in the nucleus where the OsFIT-OsIRO2 transcription complex initiates the transcription of Fe deficiency responsive genes.
Single nucleus RNASeq profiling of mouse lung: reduced dissociation bias and improved detection of rare cell types compared with single cell RNASeq
Authors: Koenitzer Jeffrey R , Wu Haojia , Atkinson Jeffrey J , Brody Steven L , Humphreys Benjamin D 
Published: March 2020

AbstractRATIONALESingle cell RNA-sequencing (scRNASeq) has led to multiple recent advances in our understanding of lung biology and pathophysiology, but utility is limited by the need for fresh samples, loss of cell types due to death or inadequate dissociation, and the induction of transcriptional stress responses during tissue digestion. Single nucleus RNASeq (snRNASeq) has addressed these deficiencies in some other tissues, but no protocol exists for lung. We sought to develop such a protocol and compare its results with scRNA-seq.METHODSSingle nucleus suspensions were prepared rapidly (45 min) from two mouse lungs in lysis buffer on ice while a single cell suspension from an additional mouse lung was generated using a combination of enzymatic and mechanical dissociation (1.5 h). Cells and nuclei were processed using the 10x Genomics platform, and following sequencing of cDNA libraries single cell data was analyzed by Seurat.RESULTS16,656 single nucleus and 11,934 single cell transcriptomes were generated. Despite reduced mRNA levels in nuclei vs. cells, gene detection rates were equivalent in snRNASeq and scRNASeq (∼1,750 genes and 3,000 UMI per cell) when mapping intronic and exonic reads. snRNASeq identified a much greater proportion of epithelial cells than scRNASeq (46% vs 2% of total), including basal and neuroendocrine cells, while reducing immune cells from 54% to 15%. snRNASeq transcripts are enriched for transcription factors and signaling proteins, with reduced detection of housekeeping genes, mitochondrial genes, and artifactual stress response genes. Both techniques improved mesenchymal cell detection over previous studies, and analysis of fibroblast diversity showed two transcriptionally distinct populations ofCol13a1+cells, termedBmper+andBrinp1+fibroblasts. To define homeostatic signaling relationships among cell types, receptor-ligand mapping of was performed for alveolar compartment cells using snRNASeq data, revealing complex interplay among epithelial, mesenchymal, and capillary endothelial cells.CONCLUSIONSingle nucleus RNASeq can be readily applied to snap frozen, archival murine lung samples, improves dissociation bias, eliminates artifactual gene expression and provides similar gene detection compared to scRNASeq.
Antibiotic prescribing records in two UK primary care electronic health record systems. Comparison of the CPRD GOLD and CPRD Aurum databases
Authors: Gulliford Martin C , Sun Xiaohui , Anjuman Thamina , Yelland Eleanor , Murray-Thomas Tarita 
Published: March 2020

ABSTRACTObjectiveWe evaluated whether recording of antibiotic prescribing across two primary care electronic health record (EHR) systems is similar. Data were analysed from the Clinical Practice Research Datalink (CPRD) databases: CPRD GOLD (Vision data) and CPRD Aurum (EMIS data).MethodsCohorts of patients were randomly sampled from both databases, stratifying by general practice, age-group and gender. All antibiotic prescriptions in 2017 were identified. Age- and sex-standardised antibiotic prescribing rates per 1,000 person years were calculated. Prescribing of individual antibiotic products and associated medical diagnosis recorded on the same date was also evaluated. English CPRD GOLD general practices were analysed as a subgroup, because all CPRD Aurum practices sampled were in England.ResultsThere were 101,360 antibiotic prescriptions among 158,305 sampled patients at 883 CPRD Aurum practices, and 112,931 prescriptions among 160,394 sampled patients at 290 CPRD GOLD practices. The age- and sex-standardised antibiotic prescribing rate in 2017 was 512.6 (95% confidence interval 510.4 to 514.9) per 1,000 person years in CPRD Aurum and 584.3 (582.1 to 586.5) per 1,000 person years in CPRD GOLD [505.2 (501.6 to 508.9) per 1,000 person years if restricted to practices in England]. The 25 most frequently prescribed antibiotic products were similar in both databases. One or more medical codes were recorded on the same date as an antibiotic prescription for 72,989 (74%) prescriptions in CPRD Aurum, 84,756 (78%) in CPRD GOLD, and 28,471 (78%) for CPRD GOLD in England. Skin, respiratory and genito-urinary tract infections were recorded for 39,035 (40%) prescriptions in CPRD Aurum, 41,326 (38%) in CPRD GOLD, with 15,481 (42%) in English CPRD GOLD practices only.ConclusionSimilar estimates for antibiotic prescribing and infection recording were found for both databases suggesting similar recording across EMIS and Vision systems. Future research on antimicrobial stewardship can be conducted in CPRD Aurum informed by previous results from CPRD GOLD. It may also be possible to combine CPRD GOLD and CPRD Aurum data in research on antibiotic prescribing.
Transmission potential of COVID-19 in Iran
Authors: Muniz-Rodriguez Kamalich , Fung Isaac Chun-Hai , Ferdosi Shayesteh R. , Ofori Sylvia K. , Lee Yiseul , Tariq Amna , Chowell Gerardo 
Published: March 2020

AbstractWe estimated the reproduction number of 2020 Iranian COVID-19 epidemic using two different methods: R0was estimated at 4.4 (95% CI, 3.9, 4.9) (generalized growth model) and 3.50 (1.28, 8.14) (epidemic doubling time) (February 19 - March 1) while the effective R was estimated at 1.55 (1.06, 2.57) (March 6-19).
Dopaminergic Co-transmission with Sonic Hedgehog Inhibits Abnormal Involuntary Movements
Authors: Malave Lauren , Zuelke Dustin R. , Uribe-Cano Santiago , Starikov Lev , Rebholz Heike , Friedman Eitan , Qin Chuan , Li Qin , Bezard Erwan , Kottmann Andreas H. 
Published: March 2020

AbstractL-Dopa induced dyskinesia (LID) is a debilitating side effect of dopamine replacement therapy for Parkinson’s Disease. The mechanistic underpinnings of LID remain obscure. Here we report that diminshed sonic hedgehog (Shh) signaling in the basal ganglia caused by the degeneration of midbrain dopamine neurons (DANs) facilitates the formation and expression of LID. We demonstrate that augmenting Shh signaling with agonists of the Shh effector Smoothened attenuates LID in mouse and macaque models of PD. Employing conditional genetic loss-of-function approaches, we show that reducing Shh secretion from DANs or Smo activity in cholinergic interneurons (CINs) promotes LID. Conversely, the selective expression of constitutively active Smo (SmoM2) in CINs is sufficient to render the sensitized aphakia model of PD resistant to LID. Furthermore, acute depletion of Shh from DANs through prolonged optogenetic stimulation in otherwise intact mice and in the absence of L-Dopa produces LID-like involuntary movements. These findings indicate that augmenting Shh signaling in the L-Dopa treated brain may be a promising and unexpected novel therapeutic approach for mitigating the dyskinetic side effects of long-term treatment with L-Dopa
Detailed point cloud data on stem size and shape of Scots pine trees
Authors: Saarinen Ninni , Kankare Ville , Yrttimaa Tuomas , Viljanen Niko , Honkavaara Eija , Holopainen Markus , Hyyppä Juha , Huuskonen Saija , Hynynen Jari , Vastaranta Mikko 
Published: March 2020

AbstractQuantitative assessment of the effects of forest management on tree size and shape has been challenging as there has been a lack of methodologies for characterizing differences and possible changes comprehensively in space and time. Terrestrial laser scanning (TLS) and photogrammetric point clouds provide three-dimensional (3D) information on tree stem reconstructions required for characterizing differences between stem shapes and growth allocation. This data set includes 3D reconstructions of stems of Scots pine (Pinus sylvestrisL.) trees from sample plots with different thinning treatments. The thinning treatments include two intensities of thinning, three thinning types as well as control (i.e. no thinning treatment since the establishment). The data set can be used in developing point clouds processing algorithms for single tree stem reconstruction and for investigating variation in stem size and shape of Scots pine trees. Additionally, it offers possibilities in characterizing the effects of various thinning treatments on stem size and shape of Scots pine trees from boreal forests.Data setZenodohttps://zenodo.org/record/3701271Data set licenseAttribution 4.0 International (CC BY 4.0)
Association of lanthipeptide genes with TnpAREPtransposases in marine picocyanobacteria
Authors: Laurenceau Raphaël , Raho Nicolas , Cariani Zev , Bliem Christina , Kearney Sean M. , Thomas Elaina , Osman Mohammed A. M. , Chisholm Sallie W. 
Published: March 2020

ABSTRACTLanthipeptides are a family of ribosomally synthesized, post-translationally modified peptides that are widespread among bacteria, typically functioning as antibacterials. The marine picocyanobacteriaProchlorococcusandSynechococcusproduce an unusual and diverse set of lanthipeptides of unknown function called prochlorosins. While well-studied model bacteria produce one or two different molecules of this type, a single picocyanobacterium can produce as many as 80; the community of picocyanobacteria in a single milliliter of seawater can collectively encode up to 10,000 prochlorosins. The molecular events that led to this expansion and diversification of the lanthipeptide repertoire in picocyanobacteria – the numerically dominant photosynthesizers in the oceans – is unknown.We present evidence for an unusual association between prochlorosin genes with a single-stranded DNA transposase belonging to the TnpAREPfamily. The genes co-occur and co-localize across the phylogeny of marine picocyanobacteria forming a distinct association pattern within genomes, most likely resulting from the transposase activity. Given the role of TnpAREPhomologs in other bacteria, we propose - based on genomic structures - that they contribute to the creation of the prochlorosin structural diversity through a diversifying recombination mechanism.Post-submission noteSince the original submission of this manuscript to bioRxiv, we have refined our phylogenetic analysis of the TnpA-REP transposases and we do not find strong evidence for or against a causal relationship between the presence of TnpA-REP transposases and the expansion and diversification of lanthipeptides genes. While the genetic association described in the manuscript remains valid, adjacent TnpA-REP and Prochlorosins do not appear phylogenetically linked, which might simply be the consequence of high rates of recombination for both genes. More genomic data are needed to untangle the driving force behind the lanthipeptide gene expansion in marine picocyanobacteria.IMPORTANCEOnly a few mechanisms have been described that promote the diversification of a targeted gene region in bacteria. We present indirect evidence that the TnpAREPtransposases associated with prochlorosins in picocyanobacteria could represent a novel such mechanism, and explain the extreme expansion and diversification of prochlorosins in this abundant marine microbe.
Unravelling the Phylogenomic Relationships of the Most Diverse African Palm GenusRaphia(Calamoideae, Arecaceae)
Authors: Helmstetter Andrew J. , Kamga Suzanne Mogue , Bethune Kevin , Lautenschläger Thea , Zizka Alexander , Bacon Christine D. , Wieringa Jan J. , Stauffer Fred , Antonelli Alexandre , Sonké Bonaventure , Couvreur Thomas L.P. 
Published: March 2020

AbstractPalms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genusRaphiahas 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material.Raphiais divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy ofRaphiais problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology.R. regalisis strongly supported as sister to all otherRaphiaspecies and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical speciesR. taedigerais supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that theRaphiaindividuals from Madagascar are potentially a distinct species different from the widely distributedR. farinifera. In conclusion, our results support the infra generic classification ofRaphiabased on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution and other eco-evolutionary aspects of this charismatic, socially and economically important palm genus.
Effects of dead conspecifics, hunger states, and seasons on the foraging behavior of the purple urchinHeliocidaris crassispina
Authors: Belleza Dominic Franco C. , Kawabata Yuuki , Toda Tatsuki , Nishihara Gregory N. 
Published: March 2020

ABSTRACTTrophic cascades exerts a powerful effect between predator and prey relationships in an ecosystem. In aquatic environments, the signals associated with predators and predation are used by prey as a cue to avoid encountering predators when foraging for food. These cues are powerful enough to control prey populations and indirectly protect primary producers. We evaluated the effects of cues associated with predation on the purple urchin,Heliocidariscrassispina and examined effects of hunger state and season using time-lapse photography, we conducted a series of manipulative andin situbehavior experiments to determine foraging behavior patterns which demonstrate behavior modification. The results suggest that starved urchins were less sensitive to predation cues when compared to normally fed urchins. Field experiments indicated that 70% of fed urchins fled when exposed to a predation cue (presence of a dead urchin), whereas all starved urchins remained regardless of the cue, supporting the results from the laboratory using the dead urchin and algae treatment cues. Sea urchin activity and feeding rates were lower in winter-spring than in summer-autumn. We suggest that hunger state has a large influence over the behavioral-response of sea urchins, while also being affected by season due to metabolic control. In general, starvation overrides predator avoidance behaviors and exposes prey species to higher risks of predation.
Sister-chromatid-sensitive Hi-C reveals the conformation of replicated human chromosomes
Authors: Mitter Michael , Gasser Catherina , Takacs Zsuzsanna , Langer Christoph C. H. , Tang Wen , Jessberger Gregor , Beales Charlie T. , Neuner Eva , Ameres Stefan L. , Peters Jan-Michael , Goloborodko Anton , Micura Ronald , Gerlich Daniel W. 
Published: March 2020

AbstractThe three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)1–3has revealed a complex genomic landscape of internal chromosome structures in vertebrate cells4–11yet how sister chromatids topologically interact in replicated chromosomes has remained elusive due to their identical sequences. Here, we present sister-chromatid-sensitive Hi-C (scsHi-C) based on nascent DNA labeling with 4-thio-thymidine. Genome-wide conformation maps of human chromosomes revealed that sister chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired, characterized by facultative heterochromatin, as well as insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister chromatid topologies and our scsHi-C technology will make it possible to dissect how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.
The time course of chromatic adaptation under immersive illumination
Authors: Gupta Gaurav , Gross Naomi , Pastilha Ruben , Hurlbert Anya 
Published: March 2020

AbstractChromatic adaptation is a major contributory mechanism to constancy, yet its extent depends on many factors - spectral, spatial and temporal - which vary between studies and hence may contribute to differences in reported constancy indices. Here, we use the achromatic adjustment method to characterise the temporal progression of chromatic adaptation under a wide range of illuminations in an immersive environment. We control both the spectral properties of the illumination at the eye and the spatial context of the adjusted surface, to disentangle global adaptation from local contrast effects. We measure the timecourse of chromatic adaptation by assessing achromatic adjustments in 6 discrete time slots over 340 seconds. We find that the change over time of the adaptation state, proximally indicated by colour constancy indices (quantified by the relative closeness of the perceptual whitepoint to the test illumination chromaticity), (a) can be modelled by a proportional rate growth function, typically requiring more than 5 minutes to stabilise; (b) depends on the contrast between the test surface and its background, specifically increasing with decreasing test-background contrast; and (c) is generally similar in both extent and rate for different test illumination chromaticities. Adaptation progression does not differ significantly between illuminations on or off the daylight locus. Our results highlight the importance of considering exposure duration and stimulus configuration, as well as the distance between the pre-adaptation (reference) and test illumination chromaticities, when using achromatic adjustment as a measure of colour constancy.
Oscillatory and aperiodic neural activity jointly predict language learning
Authors: Cross Zachariah R. , Corcoran Andrew W. , Schlesewsky Matthias , Kohler Mark. J. , Bornkessel-Schlesewsky Ina 
Published: March 2020

AbstractMemory formation involves the synchronous firing of neurons in task-relevant networks, with recent models postulating that a decrease in low frequency oscillatory activity underlies successful memory encoding and retrieval. However, to date, this relationship has been investigated primarily with face and image stimuli; considerably less is known about the oscillatory correlates of complex rule learning, as in language. Further, recent work has shown that non-oscillatory (1/f) activity is functionally relevant to cognition, yet its interaction with oscillatory activity during complex rule learning remains unknown. Using spectral decomposition and power-law exponent estimation of human EEG data (17 females, 18 males), we show for the first time that 1/fand oscillatory activity jointly influence the learning of word order rules of a miniature artificial language system. Flexible word order rules were associated with a steeper 1/fslope, while fixed word order rules were associated with a shallower slope. We also show that increased theta and alpha power predicts fixed relative to flexible word order rule learning and behavioural performance. Together, these results suggest that 1/factivity plays an important role in higher-order cognition, including language processing, and that grammar learning is modulated by different word order permutations, which manifest in distinct oscillatory profiles.
Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis
Authors: Liebers Monique , Gillet François-Xavier , Israel Abir , Pounot Kevin , Chambon Louise , Chieb Maha , Chevalier Fabien , Ruedas Rémi , Favier Adrien , Gans Pierre , Erba Elisabetta Boeri , Cobessi David , Pfannschmidt Thomas , Blanvillain Robert 
Published: March 2020

AbstractThe initial greening of angiosperm occurs upon light-activation of photoreceptors that trigger photomorphogenesis followed with the development of chloroplasts. In these semi-autonomous organelles, the construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here we show that PAP8, as an essential subunit of the plastid-encoded RNA polymerase, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 is localized and active in both plastids and the nucleus and particularly essential for the formation of late photobodies. In the albinopap8mutant, phytochrome-mediated signalling is altered, PIFs are maintained, HY5 is not stabilized, and GLK1 expression is impaired. PAP8 translocates into plastids losing its pre-sequence, interacts with the PEP, and using an unknown route or a retrograde transport, reaches the nucleus where it has the ability to interact with pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome-B-mediated signalling cascade and the reshaping of the PEP, it may coordinate nuclear gene expression with the PEP-driven chloroplastic gene expression during chloroplast biogenesis.