bluuebunny/crossref_metadata_2025_split huggingface dataset:
An anti-CRISPR protein induces strong non-specific DNA binding activity in a CRISPR-Cas complex
Authors: Lu Wang-Ting , Trost Chantel N. , Müller-Esparza Hanna , Randau Lennart , Davidson Alan R. 
Published: May 2020

ABSTRACTPhages and other mobile genetic elements express anti-CRISPR proteins (Acrs) to protect their genomes from destruction by CRISPR-Cas systems. Acrs usually block the ability of CRISPR-Cas systems to bind or cleave their nucleic acid substrates. Here, we investigate an unusual Acr, AcrIF9, that induces a gain-of-function to a type I-F CRISPR-Cas (Csy) complex, causing it to bind strongly to DNA that lacks both a PAM sequence and sequence complementarity. We show that specific and non-specific dsDNA compete for the same site on the Csy:AcrIF9 complex with rapid exchange, but specific ssDNA appears to still bind through complemetarity to the CRISPR RNA. We also demonstrate that induction of non-specific DNA-binding is a conserved property of diverse AcrIF9 homologues, implying that this activity contributes the biologically relevant function of this Acr family. AcrIF9 provides another example of the surprising variety of mechanisms by which Acrs inhibit CRISPR-Cas systems.
Conserved nicotine-activated neuroprotective pathways involve mitochondrial stress
Authors: Nourse J. Brucker , Harshefi Gilad , Marom Adi , Karmi Abdelrahaman , Caldwell Kim A. , Caldwell Guy A. , Treinin Millet 
Published: May 2020

AbstractTobacco smoking is a risk factor for several human diseases. Conversely, smoking also reduces the prevalence of Parkinson’s disease (PD), whose hallmark is degeneration ofsubstantia nigradopaminergic neurons (DNs). We useC. elegansas a model to investigate whether tobacco-derived nicotine activates nicotinic acetylcholine receptors (nAChRs) to selectively protect DNs. Using this model we demonstrate conserved functions of DN-expressed nAChRs. We find that DOP-2, a D3-receptor homolog, MCU-1, a mitochondrial calcium uniporter, and PINK-1, PTEN-induced kinase 1, are required for nicotine-mediated protection of DNs. Together, our results support involvement of calcium-dependent mitochondrial stress activation of PINK-1 in nicotine-dependent neuroprotection. This suggests that nicotine’s selective protection ofsubstantia nigraDNs is due to the confluence of two factors: first, their unique vulnerability to mitochondrial stress, which is mitigated by increased mitochondrial quality control due to PINK1 activation; and second, to their specific expression of D3 receptors.
Targeted disruption ofPparγ1promotes trophoblast endoreplication in the murine placenta
Authors: Nakano Takanari , Aochi Hidekazu , Hirasaki Masataka , Takenaka Yasuhiro , Fujita Koji , Soma Hiroaki , Kamezawa Hajime , Koizumi Takahiro , Okuda Akihiko , Murakoshi Takayuki , Shimada Akira , Inoue Ikuo 
Published: May 2020

AbstractIn murine placentas, peroxisome proliferator-activated receptor (PPAR) γ1, a nuclear receptor, is abundant at the late stage of pregnancy (E15–E16), but its functional roles are still elusive because PPARγ-full knockout embryos die early (E10). We generated mice disrupted in onlyPparγ1, one of the two major mRNA splicing variants of PPARγ1.Pparγ1-knockout embryos developed normally until 15.5 dpc, but their growth was retarded thereafter and they did not survive. At 15.5 dpc, in the wild-type placentas, intense PPARγ-immunostaining was detected in sinusoidal trophoblast giant cells (sTGCs), a cell lineage that coordinates the maternal blood microcirculation in the labyrinth, whereas they were absent in the knockouts. AlthoughPparγ1-knockout placentas were normal in morphology, we observed severely dilated maternal blood sinuses in the labyrinth. ThePparγ1-knockout sTGCs had abnormally large nuclei, an enhanced endocycling phenotype, indicating insufficient differentiation. RNA-sequencing of the placentas showed increased expression of genes coding for nucleosome assembly factors. Labyrinthine gene expressions for atypical E2Fs and cyclin E, key drivers for endocycling, were increased >3-fold. These findings suggested that PPARγ1 plays a key role in endocycle termination.
Gut bacteria mediate nutrient availabilityin Drosophiladiets
Authors: Lesperance Danielle N.A. , Broderick Nichole A. 
Published: May 2020

SummaryDrosophila melanogastergut microbes play important roles in host nutritional physiology. However, these associations are often indirect and studies typically are in the context of specialized nutritional conditions, making it difficult to discern how microbiome-mediated impacts translate to physiologically relevant conditions, in the laboratory or nature. Here, we show that on three artificial diets and a natural diet of grapes,D. melanogastergut bacteria alter protein, carbohydrates, and moisture of the food substrate. In depth analysis on one diet revealed bacteria also increase tryptophan levels. We investigate how nutrient changes impact life history and find that, while alterations to dietary protein and carbohydrates are arguably the most significant consequence of bacterial association, other factors, such as micronutrients, likely contribute to life history traits in a diet-dependent manner. Our work demonstrates that while some bacterial impacts on nutrition occur across experimental diets, others are dictated by unique dietary environments.
Transcriptomic analyses revealed the effect ofFunneliformis mosseae on differentially expressed genes inFusarium oxysporum
Authors: Zhang Xue-Qi , Bai Li , Guo Na , Cai Bai-Yan 
Published: May 2020

AbstractSoybean root rot is a typical soil-borne disease that severely affects the yield of soybean, andF. mosseae, the dominant strain of AMF in continuous cropping of soybean. The aim of this study was to providing an experimental basis for the study of the molecular mechanism underlying the alleviation of the obstacles associated with the continuous cropping of soybean by AMF. In this study,F. mosseaewas inoculated in soil planted with soybean infected withF. oxysporum. The results showed that the incidence of soybean root rot was significantly reduced after inoculation withF. mosseae. The significantly upregulated genes encoded the ABC transporter, ATP-binding/permease protein and the ABC transporter, ATP-binding protein. The significantly downregulated genes encoded chitin-binding domain proteins; key enzymes involved in metabolic pathways such as glycolysis, including class II fructose-bisphosphate aldolase and NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, glycoside hydrolase family 61 protein, which hydrolyse cellulose and hemicellulose; actin and other major components of the cytoskeleton. The DEGs were enriched in antigen processing and presentation, carbon fixation in photosynthetic organisms, glycolysis/gluconeogenesis, the MAPK signalling pathway, protein processing in the endoplasmic reticulum and RNA degradation. Inoculation withF. mosseaecould promote the growth and development of soybean and improve disease resistance. This study provides an experimental basis for further research on the molecular mechanism underlying the alleviation of challenges associated with the continuous cropping of soybean by AMF.
Characterization of Components of Resistance to Corn Stunt Disease
Authors: Oleszczuk José D. , Catalano María I. , Dalaisón Lucía , Di Rienzo Julio A. , Giménez Pecci María P. , Carpane Pablo D. 
Published: May 2020

AbstractConsidering the occasional but increasing presence of corn stunt disease in the subtropical region of Argentina, the objective of this research was to devise an effective strategy to screen disease-resistant genotypes in the absence of high and constant natural pressures. To do so, the presence of antixenosis and antibiosis as components of resistance to vectorDalbulus maidis(DeLong 1923) as well as resistance to the pathogenSpiroplasma kunkelii(Whitcomb et al. 1986) under artificial inoculation conditions were investigated in four widely-distributed maize hybrids in Argentina. The hybrids shown differences in the levels of resistance and target organisms (either the insect vector or the pathogen). Antixenosis and antibiosis toD. maidiswere observed in DK72-10. Resistance of DK79-10 toS. kunkeliiwas evidenced by a delayed onset of symptoms, and DKB390 was antixenotic toD. maidisand highly resistant toS. kunkelii. A good association was found between symptom severity and yield, but not between symptom severity and accumulation of pathogenS. kunkelii. In conclusion, the proposed methodology was efficacious and can aid the screening of resistant genotypes in breeding programs to reduce the impact of corn stunt disease, ensuring that hybrids with good resistance level will be planted by farmers whenever disease occurs.
Live imaging of hair bundle polarity acquisition in the mouse utricle demonstrates a critical timeline for transcription factor Emx2
Authors: Tona Yosuke , Wu Doris K. 
Published: May 2020

ABSTRACTThe asymmetric hair bundle on top of hair cells (HCs), comprises a kinocilium and stereocilia staircase, dictates HC directional sensitivity. The mother centriole (MC) forms the base of the kinocilium, where stereocilia are subsequently built next to it. Previously we showed that transcription factor Emx2 reverses hair bundle orientation and its expression in the mouse vestibular utricle is restricted, resulting in two regions of opposite bundle orientation (Jiang et al, 2017). Here, we investigated establishment of opposite bundle orientation in embryonic utricles by live-imaging GFP-labeled centrioles in HCs. The daughter centriole invariably migrated ahead of the MC from the center to their respective peripheral locations in HCs. Comparing HCs between utricular regions, centriole trajectories were similar but they migrated towards opposite directions, suggesting that Emx2 pre-patterned HCs prior to centriole migration. Ectopic Emx2, however, reversed centriole trajectory within hours during a critical time-window when centriole trajectory was responsive to Emx2.
Single Cell Deconstruction of Muscle Stem Cell Heterogeneity During Aging Reveals Sensitivity to the Neuromuscular Junction
Authors: Ulintz Peter J. , Larouche Jacqueline , Mohiuddin Mahir , Macias Jesus Castor , Kurpiers Sarah J. , Liu Wenxuan , Choi Jeongmoon J. , Brown Lemuel A. , Markworth James F. , de Silva Kanishka , Levi Benjamin D. , Merajver Sofia D. , Chakkalakal Joe V. , Jang Young C. , Brooks Susan V. , Aguilar Carlos A. 
Published: May 2020

AbstractDuring aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function in that impacts mobility and quality of life. Muscle loss is often associated with denervation and a loss of resident muscle stem cells (satellite cells or MuSCs), but the relationship between MuSCs and neural control has not been established. Herein, using a combination of single-cell transcriptomic analysis, high-resolution immunofluorescence imaging and transgenic young and aged mice as well as from mice with neuromuscular degeneration (Sod1-/-), a compensatory neuro-responsive function for a subset of MuSCs was identified. Genetic rescue of motor neurons in Sod1-/-mice reduced this subset of MuSCs and restored integrity of the neuromuscular junction (NMJ) in a manner akin to young muscle. Administration of severe neuromuscular trauma induced young MuSCs to specifically engraft in a position proximal to the NMJ but in aging, this behavior was abolished. Contrasting the expression programs of young and aged MuSCs after muscle injury at the single cell level, we observed distinctive gene expression programs between responses to neuro-muscular degeneration and muscle trauma. Collectively, these data reveal MuSCs sense synaptic perturbations during aging and neuro-muscular deterioration, and can exert support for the NMJ, particularly in young muscle.HighlightsTranscriptional landscapes of single satellite cells from different ages before and after injury as well as neurodegenerative models before and after nervous rescueA population of satellite cells reside in close proximity to neuromuscular synapse, which are lost with ageDenervation promotes satellite cell engraftment into post-synaptic regions of young as opposed to aged muscle
Developmental Expression of Transforming Growth Factor Induced Protein Promotes NF-Kappa-B Mediated Angiogenesis During Postnatal Lung Development
Authors: Liu Min , Iosef Cristiana , Rao Shailaja , Domingo-Gonzalez Racquel , Fu Sha , Snider Paige , Conway Simon J. , Umbach Gray S. , Heilshorn Sarah C. , Dewi Ruby E. , Dahl Mar J. , Null Donald M. , Albertine Kurt H. , Alvira Cristina M. 
Published: May 2020

AbstractRationalePulmonary angiogenesis is a key driver of alveolarization. Our prior studies showed that nuclear factor kappa-B (NFκB) promotes pulmonary angiogenesis during early alveolarization. However, the mechanisms regulating temporal-specific NFκB activation in the pulmonary vasculature are unknown.ObjectivesTo identify mechanisms that activate pro-angiogenic NFκB signaling in the developing pulmonary vasculature.MethodsProteomic analysis of the lung secretome was performed using 2D-DIGE. NFκB activation and angiogenic function was assessed in primary pulmonary endothelial cells (PEC) and TGFBI-regulated genes identified using RNA-sequencing. Alveolarization and pulmonary angiogenesis was assessed in WT and TGFBI null mice exposed to normoxia or hyperoxia. Lung TGFBI expression was determined in premature lambs supported by invasive and noninvasive respiratory support.Measurements and Main ResultsSecreted factors from the early alveolar, but not the late alveolar or adult lung, promoted proliferation and migration in quiescent, adult PEC. Proteomic analysis identified transforming growth factor beta-induced protein (TGFBI) as a protein highly expressed by myofibroblasts in the early alveolar lung that promoted PEC migration by activating NFκB via αvβ3 integrins. RNA-sequencing identifiedCsf3as a TGFBI-regulated gene that enhances nitric oxide production in PEC. Loss of TGFBI in mice exaggerated the impaired pulmonary angiogenesis induced by chronic hyperoxia, and TGFBI expression was disrupted in premature lambs with impaired alveolarization.ConclusionsOur studies identify TGFBI as a developmentally-regulated protein that promotes NFκB-mediated angiogenesis during early alveolarization by enhancing nitric oxide production. We speculate that dysregulation of TGFBI expression may contribute to diseases marked by impaired alveolar and vascular growth.
Beyond rates: Time-varying dynamics of high frequency oscillations as a biomarker of the seizure onset zone
Authors: Nunez Michael D. , Charupanit Krit , Sen-Gupta Indranil , Lopour Beth A. , Lin Jack J. 
Published: May 2020

AbstractObjectiveHigh frequency oscillations (HFOs) recorded by intracranial electrodes have generated excitement for their potential to help localize epileptic tissue for surgical resection. However, the number of HFOs per minute (i.e. the HFO “rate”) is not stable over the duration of intracranial recordings; for example, the rate of HFOs increases during periods of slow-wave sleep. Moreover, HFOs that are predictive of epileptic tissue may occur in oscillatory patterns due to phase coupling with lower frequencies. Therefore, we sought to further characterize between-seizure (i.e. “interictal”) HFO dynamics both within and outside the seizure onset zone (SOZ).ApproachUsing long-term intracranial EEG (mean duration 10.3 hours) from 16 patients, we automatically detected HFOs using a new algorithm. We then fit a hierarchical Negative Binomial model to the HFO counts. To account for differences in HFO dynamics and rates between sleep and wakefulness, we also fit a mixture model to the same data that included the ability to switch between two discrete brain states that were automatically determined during the fitting process. The ability to predict the SOZ by model parameters describing HFO dynamics (i.e. clumping coefficients and coefficients of variation) was assessed using receiver operating characteristic curves.Main resultsParameters that described HFO dynamics were predictive of SOZ. In fact, these parameters were found to be more consistently predictive than HFO rate. Using concurrent scalp EEG in two patients, we show that the model-found brain states corresponded to (1) non-REM sleep and (2) awake and rapid eye movement sleep. However the brain state most likely corresponding to slowwave sleep in the second model improved SOZ prediction compared to the first model for only some patients.SignificanceThis work suggests that delineation of seizure onset zone with interictal data can be improved by the inclusion of time-varying HFO dynamics.1.Novelty & SignificanceThe rate of high frequency oscillations (HFOs), measured as number per minute, is a biomarker of the seizure onset zone (SOZ) in epilepsy patients. However, the rate changes over time and HFO occurrence can be phase-coupled to slow oscillations. Here we show, through novel application of negative binomial models to HFO count data, that HFO temporal dynamics are a biomarker of the SOZ and are superior to HFO rate. Specifically, more random occurrence of HFOs predicted SOZ, as opposed to events clustered in time. This suggests that consideration of HFO temporal dynamics can improve SOZ localization for epilepsy surgery.
MR Imaging Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer
Authors: Hillestad Tiril , Hompland Tord , Fjeldbo Christina S. , Skingen Vilde E. , Salberg Unn Beate , Aarnes Eva-Katrine , Nilsen Anja , Lund Kjersti V. , Evensen Tina S. , Kristensen Gunnar B. , Stokke Trond , Lyng Heidi 
Published: May 2020

AbstractTumor hypoxia levels range from mild to severe and have different biological and therapeutical consequences, but are not easily assessable in patients. We present a method based on diagnostic dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) that visualizes a continuous range of hypoxia levels in tumors of cervical cancer patients. Hypoxia images were generated using an established approach based on pixel-wise combination of the DCE-MRI parametersνeandKtrans, reflecting oxygen consumption and supply, respectively. An algorithm to retrieve hypoxia levels from the images was developed and validated in 28 xenograft tumors, by comparing the MRI-defined levels with hypoxia levels derived from pimonidazole stained histological sections. We further established an indicator of hypoxia levels in patient tumors based on expression of nine hypoxia responsive genes. A strong correlation was found between these indicator values and the MRI-defined hypoxia levels in 63 patients. Chemoradiotherapy outcome of 74 patients was most strongly predicted by moderate hypoxia levels, whereas more severe or milder levels were less predictive. By combining gene expression profiles and MRI-defined hypoxia levels in cancer hallmark analysis, we identified a distribution of levels associated with each hallmark; oxidative phosphorylation and G2/M checkpoint were associated with moderate hypoxia, and epithelial-to-mesenchymal transition and inflammatory responses with significantly more severe levels. At the mildest levels, interferon response hallmarks, together with stabilization of HIF1A protein by immunohistochemistry, appearred significant. Thus, our method visualizes the distribution of hypoxia levels within patient tumors and has potential to distinguish levels of different prognostic and biological significance.
Novel role of AGT gene in aplastic anaemia among paediatric patients based on gene expression profiling
Authors: Adhikari Sarmistha , Mandal Paramita 
Published: May 2020

AbstractObjectivesSevere aplastic anemia is characterized by a hypocellular bone marrow and peripheral cytopenia. Mesenchymal stem cells (MSCs) play a crucial role in haematopoietic stem cells (HSCs) development and the microenvironment suitable for haematopoiesis. Investigation of the therapeutic targets by paediatric patient-specific gene expression analysis of the MSCs can be important for diagnosis.MethodsThe study was based on freely available miRNA and host gene expression in NCBI GEO dataset. Microarray based gene expression profiles (GSE33812) of MSCs for five paediatric aplastic anaemia patients and healthy controls were generated using Agilent-014850 platform and the data was downloaded from the database.ResultsMSCs gene expression profiling distinguished between healthy controls, children with aplastic anemia. Angioteninogen (AGT) gene involved in ERK1/ERK2 cascade, cyotokine secretion, metabolic processes was strongly down-regulated among all the patients with aplastic anemia. Emerging role of various transcription factors binding to this gene was identified as a new avenue of therapeutic application.ConclusionsAs a potential diagnostic tool, patient-specific gene expression profiling of MSCs made it possible to make the difficult diagnosis of most patients with aplastic anemia.
The eve of the 1896 revolution: experiencing Philippine history through immersive and gamified learning
Authors: Moscoso Mildred O. , de Jesus Ana Katrina P. , Abagat Renz Frances D. , Centeno Edmund G. , Custodio Rhodora Ramonette D.V. , Embate John Mervin L. , Pine Elijah Jesse Mendoza , Belano Zoilo D. , Crudo Eugene Raymond P. , Lopega Diosdado B. , Mangubat Lexter J. 
Published: May 2020

PurposeKatipuneros RPG: Bisperas ng Himagsikan (Katipuneros RPG: The Eve of the Revolution) is an immersive and gamified theater that engages its “audiences” in the initiation rites of a secret revolutionary movement in the Philippines in 1896. This descriptive qualitative research evaluates such experiential approach to learning history by investigating the experiences and insights of a group of students from the University of the Philippines Los Baños (UPLB), who participated in Katipuneros RPG.Design/methodology/approachTextual data obtained from the participants' reflection papers and focus group discussion transcripts were analyzed using open and axial coding.FindingsThree key themes summarized the participants' learning experiences as they went through the play, as follows: (1) Katipuneros RPG as an immersive, interactive and intrinsically motivating medium for learning history; (2) the knowledge, values and skills that served as facilitating factors for their learning and (3) the insights the participants gained about history and life in general.Practical implicationsThe research argues that in Katipuneros RPG, learners take on a more active role in studying history as the “teacher” vanishes in lieu of a learning system the allows students to think critically, reflect and collaborate. The approach integrates elements of development theater, immersive play and gamified learning, as well as the principles of constructivist, play-based and multi-sensorial learning.Social implicationsAs an innovative learning tool, it is a viable medium to teach history in the current socio-political context of the Philippines.Originality/valueThe study hopes to contribute to literature on pedagogical approaches for teaching and learning history through immersive environments.