bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field margins as substitute habitat for the conservation of birds in agricultural wetlands
Authors: Pierre Mallet , Arnaud Béchet , Clélia Sirami , François Mesléard , Thomas Blanchon , François Calatayud , Thomas Dagonet , Elie Gaget , Carole Leray , Thomas Galewski 
Published: May 2022

AbstractBreeding birds in agricultural landscapes have declined considerably since the 1950s and the beginning of agricultural intensification in Europe. Given the increasing pressure on agricultural land, it is necessary to identify conservation measures that consume little productive land. We tested the compensation hypothesis which states that field margins may represent substitute habitats for bird species in agricultural wetlands. We monitored bird species in 86 crop fields in rice paddy landscapes of Camargue (southern France), a wetland of international importance for birds. We investigated whether the area of three types of field margins (reed strips, grass strips and hedgerows) within a 500 meter buffer around the centroid of each crop fields had an effect on the abundance of bird species from three groups defined based on their primary habitat (reedbeds, grasslands, and forest edge species). We controlled for the area of each type of semi-natural habitat (wetlands, grasslands, and woodlands), crop diversity (rice, wheat, alfalfa, rape, and market gardening) and mean crop field size. Results show partial support of the compensation hypothesis with species-dependent responses to primary and substitute habitat area. Some species within the reedbed and grassland bird guilds are favored by the area of their primary habitat as well as by the area of field margins, in line with the compensation hypothesis. Eurasian reed warbler is favored by the area of both wetlands and reed strips. Corn bunting is favored by grassland and grass strip areas. We could not confirm the compensation hypothesis for other species. However, this may be due to the fact that most of these species did not respond to their primary habitat. These results therefore suggest that field margins may represent substitute habitats for some species but further studies, in contexts where species are strongly associated with their primary habitat, would be needed to confirm the generality of this hypothesis. Our results also suggest that species response to increasing the area of a field margin type may vary among guilds and even within guilds. Therefore, it may be difficult to favor all species within a given landscape and management actions may need to be tailored to whichever species are locally associated with the highest conservation priority. To tackle this challenge, it may be necessary to design landscape management actions at different spatial scales.
Tbx2 is essential for cochlear inner hair cell development and regeneration
Authors: Bi Zhenghong , Li Xiang , Ren Minhui , Gu Yunpeng , Zhu Tong , Li Shuting , Wang Guangqin , Sun Suhong , Sun Yuwei , Liu Zhiyong 
Published: May 2022

AbstractAtoh1 is essential for the development of outer hair cells (OHCs) and inner hair cells (IHCs) in the mammalian cochlea. Whereas Ikzf2 is necessary for OHC development, the key gene for IHC development remains unknown. We found that deleting Tbx2 in neonatal IHCs led to their trans-differentiation into OHCs, by repressing 26.7% of IHC and inducing 56.3% of OHC genes, including Ikzf2. More importantly, persistent expression of Tbx2 together with transient Atoh1 effectively reprogramed non-sensory supporting cells into new IHCs expressing functional IHC marker vGlut3. The differentiation status of these new IHCs is much more advanced than those previously reported. Thus, Tbx2 is essential for IHC development, and its co-upregulation with Atoh1 in supporting cells represents a new approach for treating IHC degeneration-related deafness.
Auxin Plays a Role in the Adaptation of Rice to Anaerobic Germination and Seedling Establishment
Authors: Lee Kuo-Wei , Chen Jeremy J.W. , Wu Chung-Shen , Chang Ho-Chun , Chen Hong-Yue , Kuo Hsin-Hao , Lee Ya-Shan , Chang Yan-Lun , Chang Hung-Chia , Shiuea Shiau-Yu , Wu Yi-Chen , Ho Yi-Cheng , Chen Peng-Wen 
Published: May 2022

AbstractAuxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies have shown that excessive levels of IAA frequently cause the inhibition of plant growth and development. In the present study, the high-level accumulation of endogenous IAA is observed under submergence in the dark, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167-ARF-GH3 pathway. TheOsGH3-8encodes an IAA-amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressingOsGH3-8increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. The present study reveals that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance.
An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia
Authors: Provez Lien , Van Puyvelde Bart , Corveleyn Laura , Demeulemeester Nina , Verhelst Sigrid , Lintermans Béatrice , Daled Simon , Roels Juliette , Clement Lieven , Martens Lennart , Deforce Dieter , Van Vlierberghe Pieter , Dhaenens Maarten 
Published: May 2022

AbstractThe holistic nature of omics studies makes them ideally suited to generate hypotheses on health and disease. Sequencing-based genomics and mass spectrometry (MS)-based proteomics are linked through epigenetic regulation mechanisms. However, epigenomics is currently mainly focused on DNA methylation status using sequencing technologies, while studying histone posttranslational modifications (hPTMs) using MS is lagging, partly because reuse of raw data is impractical. Yet, targeting hPTMs using epidrugs is an established promising research avenue in cancer treatment. Therefore, we here present the most comprehensive MS-based preprocessed hPTM atlas to date, including 21 T-cell acute lymphoblastic leukemia (T-ALL) cell lines. We present the data in an intuitive and browsable single licensed Progenesis QIP project and provide all essential quality metrics, allowing users to assess the quality of the data, edit individual peptides, try novel annotation algorithms and export both peptide and protein data for downstream analyses, exemplified by the PeptidoformViz tool. This data resource sets the stage for generalizing MS-based histone analysis and provides the first reusable histone dataset for epidrug development.
Bayesian prediction of multivariate ecology from phenotypic data yields new insights into the diets of extant and extinct taxa
Authors: Wisniewski Anna L. , Nations Jonathan A. , Slater Graham J. 
Published: May 2022

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.
Condensation of the fusion focus by the intrinsically disordered region of the formin Fus1 is essential for cell-cell fusion
Authors: Billault-Chaumartin Ingrid , Muriel Olivia , Michon Laetitia , Martin Sophie G 
Published: May 2022

SummarySpatial accumulation of secretory vesicles underlies various cellular processes, such as neurotransmitter release at neuronal synapses [1], hyphal steering in filamentous fungi [2, 3], and local cell wall digestion preceding the fusion of yeast gametes [4]. Secretory vesicles transported on actin filaments by myosin V motors form clusters that serve as pool for local content release. During fission yeast Schizosaccharomyces pombe gamete fusion, the actin fusion focus assembled by the formin Fus1 concentrates secretory vesicles carrying cell wall digestive enzymes [5-7]. Focus position and coalescence are controlled by local signalling and actin-binding proteins to prevent inappropriate cell wall digestion that would cause lysis [6, 8-10], but the mechanisms of focusing have been elusive. Here, we show that the regulatory N-terminus of Fus1 contains an intrinsically disordered region (IDR) that mediates Fus1 condensation in vivo and forms dense assemblies that exclude other macromolecules. Fus1 lacking its IDR fails to condense in a tight focus and causes cell lysis during attempted cell fusion. Remarkably, replacement of Fus1 IDR with a heterologous low-complexity region that forms liquid condensates fully restores Fus1 condensation and function. By contrast, replacement of Fus1 IDR with a domain that forms more stable oligomers restores condensation but poorly supports cell fusion, suggesting that condensation is tuned to yield a structure selectively permeable for secretory vesicles. We propose that condensation of actin structures by an intrinsically disordered region may be a general mechanism for actin network organisation and the selective local concentration of secretory vesicles.
Insights into Long-term Acclimation Strategies of Grapevines in Response to Multi-decadal Cyclical Drought
Authors: Nagahatenna Dilrukshi S. K. , Furlan Tarita S. , Edwards Everard J. , Ramesh Sunita A. , Pagay Vinay 
Published: May 2022

AbstractThe Australian wine industry is currently under pressure to sustain its profitability due to climate change. Therefore, there is a pressing need to explore grapevine genetic diversity and identify superior clones with improved drought resistance. We previously characterised more than 15,000 dry-farmed (for over 65 years) Cabernet Sauvignon clones in a vineyard and identified three drought-tolerant (DT) clones, which can maintain significantly higher intrinsic water use efficiency (WUEi) under limited soil moisture than drought-sensitive (DS) clones. To understand whether DT clones grown under multi-decadal cyclical drought can prime their vegetatively-propagated clonal progenies for future drought events, in this study, all DT and DS vegetative progenies were propagated with commercial clones in the glasshouse. Their physiological and molecular responses were investigated under well-watered and two recurrent drought (D1 and D2) conditions. We observed that concentration of a natural priming agent, γ-amino butyric acid (GABA), were significantly higher in all DT progenies relative to other progenies under drought. Both commercial and DT progenies exhibited improved gas exchange, photosynthetic performance and WUEi under recurrent drought events relative to DS progenies. Our results suggest that DT progenies have adapted to be in a “primed state” to withstand future drought events.
Autonomous untethered microinjectors for gastrointestinal delivery of insulin
Authors: Ghosh Arijit , Liu Wangqu , Li Ling , Pahapale Gayatri , Choi Si Young , Xu Liyi , Huang Qi , Selaru Florin M. , Gracias David H. 
Published: May 2022

AbstractThe delivery of macromolecular drugs via the gastrointestinal (GI) tract is challenging. Macromolecular drugs display low stability and poor absorption across the intestinal epithelium. While permeation-enhancing drug delivery methods can increase the bioavailability of low molecular weight drugs, the effective delivery of high molecular weight drugs across the tight epithelial cell junctions remains a formidable challenge. Here, we describe autonomous microinjectors that can efficiently penetrate the GI mucosa and deliver insulin systemically. In addition, we performed in vitro studies to characterize insulin release and the penetration capacity of microinjectors and measure in vivo release of insulin in live rats. We found that the microinjectors administered within the luminal GI tract could deliver insulin trans-mucosally to the systemic circulation at similar levels to intravenously administered insulin. Due to their small size, tunability in sizing and dosing, wafer-scale fabrication, and parallel, autonomous operation, we anticipate that these novel microinjectors could significantly advance drug delivery across the GI tract mucosa to the systemic circulation.
The iron-sulfur cluster is critical for DNA binding by human DNA polymerase ε
Authors: Lisova Alisa E. , Baranovskiy Andrey G. , Morstadt Lucia M. , Babayeva Nigar D. , Stepchenkova Elena I. , Tahirov Tahir H. 
Published: May 2022

ABSTRACTDNA polymerase ε (Polε) is a key enzyme for DNA replication in eukaryotes. It is attached to a helicase and performs DNA synthesis on the leading strand. Recently it was shown that the catalytic domain of yeast Polε (PolεCD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we have shown that human PolεCD (hPolεCD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPolεCD produced in insect cells contains an eight-fold-lower level of iron. Interestingly, the iron content correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPolε interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding and, therefore, DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. In addition, we performed kinetic and binding studies of hPolεCD. The binding studies demonstrated low affinity of hPolεCD to DNA and a strong effect of salt concentration on stability of the hPolεCD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s-1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 μM. This work provides notable insight into the role of a [4Fe-4S] cluster in Polε function.
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription
Authors: Reed Kathleen S. M. , Davis Eric S. , Bond Marielle L. , Cabrera Alan , Thulson Eliza , Quiroga I. Yoseli , Cassel Shannon , Woolery Kamisha T. , Hilton Isaac , Won Hyejung , Love Michael I. , Phanstiel Douglas H. 
Published: May 2022

SUMMARYTo infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation. Enhancers and genes connected by loops exhibited stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. Changes in acetylation at looped distal enhancers preceded changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, while lost loops were often accompanied by high levels of transcription with the loop boundaries themselves. Taken together, these results are consistent with a reciprocal relationship in which loops can facilitate increased transcription by connecting promoters to distal enhancers while high levels of transcription can impede loop formation.HIGHLIGHTSLPS + IFNγ triggers genome-wide changes in chromatin looping, enhancer acetylation, and gene expressionLooped enhancer-promoter pairs exhibit ordered and correlated changes in acetylation and expressionChanges in gene expression exhibit a directional bias at differential loop anchorsLost loops are associated with high levels of transcription within loop boundaries
Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals
Authors: Bilgic Merve , Wu Quan , Suetsugu Taeko , Shitamukai Atsunori , Tsunekawa Yuji , Shimogori Tomomi , Kadota Mitsutaka , Nishimura Osamu , Kuraku Shigehiro , Kiyonari Hiroshi , Matsuzaki Fumio 
Published: May 2022

ABSTRACTThe diversity of neural stem cells is a hallmark of the cerebral cortex development in gyrencephalic mammals, such as Primates and Carnivora. Among them, ferrets are a good model for mechanistic studies. However, information on their neural progenitor cells (NPC), termed radial glia (RG), is limited. Here, we surveyed the temporal series of single-cell transcriptomes of progenitors regarding ferret corticogenesis and, found a conserved diversity and temporal trajectory between human and ferret NPC, despite the large timescale difference. We found truncated RG (tRG) in ferret cortical development, a progenitor subtype previously described in humans. The combination ofin silicoandin vivoanalyses identified that tRG differentiate into both ependymal and astrogenic cells. Via transcriptomic comparison, we predict that this is also the case in humans. Our findings suggest that tRG plays a role in the formation of adult ventricles, thereby providing the architectural bases for brain expansion.
Development of recombinant monoclonal antibodies targeting conserved VlsE epitopes in Lyme disease pathogens
Authors: Li Li , Di Lia , Akther Saymon , Zeglis Brian M. , Qiu Weigang 
Published: May 2022

AbstractVlsE (variable major protein-likesequence,expressed) is an outer surface protein of the Lyme disease pathogen (Borreliellaspecies) and a key diagnostic biomarker of Lyme disease. However, the high sequence variability of VlsE poses a challenge to the development of consistent VlsE-based diagnostics and therapeutics. In addition, the standard diagnostic protocols detect immunoglobins elicited by the Lyme pathogen, not the presence of pathogen or its derived antigens. Here we describe the development of recombinant monoclonal antibodies (rMAbs) that bind specifically to conserved epitopes on VlsE. We first quantified amino-acid sequence variability encoded by thevlsgenes from thirteenB. burgdorferigenomes by evolutionary analyses. We showed broad inconsistencies of the sequence phylogeny with the genome phylogeny, indicating rapid gene duplications, losses, and recombination at thevlslocus. To identify conserved epitopes, we synthesized peptides representing five long conserved invariant regions (IRs) on VlsE. We tested the antigenicity of these five IR peptides using sera from three mammalian host species including human patients, the natural reservoir white-footed mouse (Peromyscus leucopus), and VlsE-immunized New Zealand rabbits (Oryctolagus cuniculus). The IR4 and IR6 peptides emerged as the most antigenic and reacted strongly with both the human and rabbit sera, while all IR peptides reacted poorly with sera from natural hosts. Four rMAbs binding specifically to the IR4 and IR6 peptides were identified, cloned, and purified. Given their specific recognition of the conserved epitopes on VlsE, these IR-specific rMAbs are promising diagnostic and theragnostic agents for direct detection of Lyme disease pathogens regardless of strain heterogeneity.
Polyimidazolium protects against an invasive clinical isolate of Salmonella Typhimurium
Authors: Mon Khin K. Z. , Si Zhangyong , Chan-Park Mary B. , Kenney Linda J. 
Published: May 2022

ABSTRACTFrequent outbreaks of Salmonella Typhimurium infection in both the animal and human population with potential for zoonotic transmission pose a significant threat to the public health sector. The rapid emergence and spread of more invasive multidrug-resistant clinical isolates of Salmonella further highlight the need for the development of new drugs with effective broad-spectrum bactericidal activities. Synthesis and evaluation of main-chain cationic polyimidazolium 1 (PIM1) against several gram-positive and gram-negative bacteria have previously demonstrated the efficacy profile of PIM1. The present study focuses on antibacterial and anti-biofilm activities of PIM1 against Salmonella both in vitro and in ovo setting. In vitro, PIM1 exhibited bactericidal activity against all tested three strains of Salmonella at a low dosage of 8 μg/ml. Anti-biofilm activity of PIM1 was evident with complete inhibition for the initial attachment of biofilms at 16 μg/ml and degradation of pre-formed biofilms in a dose-dependent manner. During the host cell infection process, PIM1 reduces extracellular bacterial adhesion and invasion rates to limit the establishment of infection. Once intracellular, the drug-resistant strain was tolerant and protected from PIM1 treatment. In a chicken egg infection model, PIM1 exhibited therapeutic activity for both Salmonella strains with stationary-phase and exponential-phase inocula. Moreover, PIM1 showed a remarkable efficacy against the stationary phase inocula of drug-resistant Salmonella by eliminating the bacteria burden in >50% of infected chicken egg embryos. Collectively, PIM1 has demonstrated its potential as a drug candidate for treatment of Salmonella infections, as well as a solution to tackle egg contamination issues on poultry farms.