bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity-based cell sorting reveals resistance of functionally degenerateNitrospiraduring a press disturbance in nitrifying activated sludge
Authors: Madill Maxwell B.W. , Luo Yaqian , Sampara Pranav , Ziels Ryan M. 
Published: April 2021

AbstractManaging and engineering activated sludge wastewater treatment microbiomes for low-energy nitrogen removal requires process control strategies to stop the oxidation of ammonium at nitrite. Our ability to out-select nitrite oxidizing bacteria (NOB) from activated sludge is challenged by their metabolic and physiological diversity, warranting measurements of theirin situphysiology and activity under selective growth pressures. Here, we examined the stability of nitrite oxidation in activated sludge during a press disturbance induced by treating a portion of return activated sludge with a sidestream flow containing free ammonia (FA) at 200 mg NH3-N/L. The nitrite accumulation ratio peaked at 42% by day 40 in the experimental bioreactor with the press disturbance, while it did not increase in the control bioreactor. A subsequent decrease in nitrite accumulation within the experimental bioreactor coincided with shifts in dominantNitrospira16S rRNA amplicon sequence variants (ASVs). We applied bioorthogonal non-canonical amino acid tagging (BONCAT) coupled with fluorescence activated cell sorting (FACS) to investigate changes in the translational activity of NOB populations throughout batch exposure to FA. BONCAT-FACS confirmed that the singleNitrospiraASV washed-out of the experimental bioreactor had reduced translational activity following exposure to FA, whereas the twoNitrospiraASVs that emerged after process acclimation were not impacted by FA. Thus, the coexistence of functionally degenerate and physiologically resistantNitrospirapopulations provided resilience to the nitrite-oxidizing function during the press disturbance. These results highlight how BONCAT-FACS can resolve ecological niche differentiations within activated sludge and inform strategies to engineer and control microbiome function.ImportanceNitrogen removal from activated sludge wastewater treatment systems is an energy-intensive process due to the large aeration requirement for nitrification. This energy footprint could be minimized with engineering control strategies that wash-out nitrite oxidizing bacteria (NOB) to limit oxygen demands. However, NOB populations can have a high degree of physiological diversity, and it is currently difficult to decipher the behavior of individual taxa during applied selective pressures. Here, we utilized a new substrate analog probing approach to measure the activity of NOB at the cellular translational level in the face of an applied press disturbance to the activated sludge process. Substrate analog probing corroborated the time-series reactor sampling, showing that coexisting and functionally redundantNitrospiraprovided resilience to the nitrite oxidation process. Taken together, these results highlight how substrate analog approaches can illuminatein situecophysiologies within shared niches, and can inform strategies to improve microbiome engineering and management.
Membrane surfaces regulate assembly of a ribonucleoprotein condensate
Authors: Snead Wilton T. , Gerbich Therese M. , Seim Ian , Hu Zhongxiu , Gladfelter Amy S. 
Published: April 2021

AbstractBiomolecular condensates organize biochemistry in time and space, yet little is known about how cells control either the position or scale of these assemblies. In cells, condensates often appear as dispersed, relatively small assemblies that do not grow (coarsen) into a single droplet despite their propensity to coalesce. Here we report that ribonucleoprotein condensates of the Q-rich protein Whi3 interact with the endoplasmic reticulum, prompting us to hypothesize that membrane association controls the position and size of condensates. Reconstitution of Whi3 condensates on supported lipid bilayers reveals that association with a diffusive lipid surface promotes condensation at both physiological ionic strength and protein concentration. Notably, these assemblies rapidly arrest, matching size distributions seen in cells. The timing of the arrest is influenced by the ordering of protein-protein and protein-RNA interactions and controlled by the slow diffusion of complexes induced by the membrane. This slowed diffusion limits both transfer of small protein-RNA complexes between condensates and their coalescence, thus driving coarsening to arrest. Our experiments reveal a tradeoff between locally-enhanced protein concentration at membranes, which favors condensation, and an accompanying reduction in diffusion, which restricts coarsening. Thus, membranes can maintain a population of small condensates in the absence of active mechanisms. Given that many condensates are bound to endomembranes, we predict that the biophysical properties of lipid bilayers are key for controlling condensate sizes throughout the cell.One sentence summaryAssembly on a membrane surface positions and scales biomolecular condensates by controlling relative diffusion rates of proteins and nucleic acids.
Transposable element profiles reveal cell line identity and loss of heterozygosity inDrosophilacell culture
Authors: Han Shunhua , Basting Preston J. , Dias Guilherme , Luhur Arthur , Zelhof Andrew C. , Bergman Casey M. 
Published: April 2021

ABSTRACTCell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabelling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here we leverage the classical observation that transposable elements (TEs) proliferate in culturedDrosophilacells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance ofDrosophilacell lines. We identify multiple cases where TE profiles clarify the origin ofDrosophilacell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of LTR retrotransposon families are necessary to markDrosophilacell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome shotgun sequencing data (called ngs_te_mapper2), which revealed copy-neutral loss of heterozygosity as a mechanism shaping the unique TE profiles that identifyDrosophilacell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines inDrosophilaand other organisms.
Design of a new effector recognition specificity in a plant NLR immune receptor by molecular engineering of its integrated decoy domain
Authors: Cesari Stella , Xi Yuxuan , Declerck Nathalie , Chalvon Véronique , Mammri Léa , Pugnière Martine , Henriquet Corinne , de Guillen Karine , Padilla André , Kroj Thomas 
Published: April 2021

SUMMARYPlant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that specifically recognize pathogen effectors and induce immune responses. Designing artificial NLRs with new effector recognition specificities is a promising prospect for sustainable, knowledge-driven crop protection. However, such strategies are hampered by the complexity of NLR function. Here, we tested whether molecular engineering of the integrated decoy domain (ID) of an NLR could extend its recognition spectrum to a new effector. To this aim, we relied on the detailed molecular knowledge of the recognition of distinctMagnaporthe oryzaeMAX (MagnaportheAVRs and ToxB-like) effectors by the rice NLRs RGA5 and Pikp-1. For both NLRs, effector recognition involves physical binding to their HMA (Heavy Metal-Associated) IDs. However, AVR-PikD, the effector recognized by Pikp-1, binds to a completely different surface of the HMA domain compared to AVR-Pia and AVR1-CO39, recognized by RGA5. By introducing into the HMA domain of RGA5 the residues of the Pikp-1 HMA domain involved in AVR-PikD binding, we created a high-affinity binding surface for this new effector. In theNicotiana benthamianaheterologous system, RGA5 variants carrying this engineered binding surface still recognize AVR-Pia and AVR1-CO39, but also perceive the new ligand, AVR-PikD, resulting in the activation of immune responses. Therefore, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs. However, it pinpoints significant knowledge gaps that limit the full deployment of this NLR-ID engineering strategy and provides hypotheses for future research on this topic.
Predicting memory from the network structure of naturalistic events
Authors: Lee Hongmi , Chen Janice 
Published: April 2021

ABSTRACTWhen we remember events, we often do not only recall individual events, but also the connections between them. However, extant research has focused on how humans segment and remember discrete events from continuous input, with far less attention given to how the structure of connections between events impacts memory. Here we conduct a functional magnetic resonance imaging study in which subjects watch and recall a series of realistic audiovisual narratives. By transforming narratives into networks of events, we demonstrate that more central events—those with stronger semantic or causal connections to other events—are better remembered. During encoding, central events evoke larger hippocampal event boundary responses associated with memory formation. During recall, high centrality is associated with stronger activation in cortical areas involved in episodic recollection, and more similar neural representations across individuals. Together, these results suggest that when humans encode and retrieve complex real-world experiences, the reliability and accessibility of memory representations is shaped by their location within a network of events.
Association of complicated appendicitis on the risk of later in vitro fertilization treatment requirement and ectopic pregnancy: a nationwide cohort study
Authors: Männistö Jaana , Sammalkorpi Henna , Niinimäki Maarit , Mentula Maarit , Mentula Panu 
Published: April 2021

AbstractIntroductionA population‐based register study utilizing three Finnish National Registers was carried out to determine whether uncomplicated appendicitis, complicated appendicitis and appendectomy without appendicitis are associated with a subsequent risk of requiring in vitro fertilization (IVF) treatment or a risk of ectopic pregnancy among reproductive‐age women.Material and methodsA total of 23 997 women who underwent appendectomy for uncomplicated or complicated appendicitis or for nonspecific abdominal pain or who had nonspecific abdominal pain without surgical procedures between 2000 and 2012 were included in the study. The later risks of IVF treatment requirement and ectopic pregnancy were assessed after uncomplicated appendicitis, complicated appendicitis and appendectomy without appendicitis. Women with nonspecific abdominal pain without surgical procedures served as the reference group.ResultsThe rates of later IVF treatment after uncomplicated appendicitis, complicated appendicitis and appendectomy without appendicitis were low (2.1%, 2.5% and 2.3%, respectively; p = 0.681). Neither appendicitis nor appendectomy was associated with the risk of requiring IVF treatment. The rate of ectopic pregnancy after uncomplicated and complicated appendicitis was very low (0.8%). Women with uncomplicated appendicitis had a significantly lower risk of ectopic pregnancy compared with patients with nonspecific abdominal pain.ConclusionsAppendicitis, whether complicated or uncomplicated, and appendectomy without appendicitis does not increase the risk of requiring later IVF treatment or the risk of ectopic pregnancy.
Grassland management and land use history shape species composition and diversity in Transylvanian semi‐natural grasslands
Authors: Kuhn Thomas , Domokos Péter , Kiss Réka , Ruprecht Eszter 
Published: April 2021

AbstractAimsSemi‐natural grasslands are among the most biodiverse habitats in Europe, and they are of great conservation and agricultural value. However, changes in land use like grazing intensification and the cessation of traditional management have dramatic effects on the extent and biodiversity of these ecosystems. In this study we investigated how current management practices and land use history shape species composition and diversity patterns in semi‐natural grasslands of the Eastern hills of the Cluj region.LocationEastern hills of Cluj (“Dealurile Clujului de Est” ‐ ROSCI0295) Natura 2000 conservation site and close surroundings, Transylvania, Romania.MethodsWe surveyed plots in extensively and intensively grazed grasslands, grasslands mown by hand or heavy machinery, and abandoned grasslands. To quantify grassland continuity, we analysed a series of historical cadastral and more current maps ranging from the 18th to the 21st century.ResultsSpecies composition was significantly influenced by current management, grassland continuity and environmental factors. Mown and extensively grazed grasslands had more grassland and forest edge specialists than abandoned and intensively grazed grasslands. In addition, there was a positive relationship between the number of grassland specialists, forest edge species and grassland continuity, while the number of ruderal species related negatively to grassland continuity. The highest diversity values were recorded in traditionally mown grasslands. However, diversity‐related variables were poorly reflected by grassland continuity.ConclusionsThis study provides evidence that short‐term abandonment may not be as detrimental for grasslands as often suggested, and intensive grazing results in the greatest loss in species diversity. Grassland continuity tightly influences the persistence of grassland specialist species. Thus, we recommend land use history to be included in the selection and identification of high‐nature‐value grasslands by prioritizing conservation efforts for older grasslands.
Intravascular pseudolymphomatous angiosarcoma: A new finding potentially mistaken for intravascular lymphoma
Authors: Goyal Amrita , Tope Whitney , Murugan Paari , Jacobson‐Dunlop Erick , Miller Daniel D. 
Published: April 2021

AbstractPseudolymphomatous infiltrates associated with angiosarcoma are a rarely reported phenomenon. Recognition of this reactive process is critical to making an accurate diagnosis, both in diagnosing the angiosarcoma and in avoiding an incorrect diagnosis of lymphoma. Here, we present a novel histopathologic pattern, angiosarcoma with a prominently intravascular atypical lymphoid component, mimicking intravascular T‐cell lymphoma. Interestingly, serial biopsies in this case revealed a progressive increase in lymphocyte density and intravascular component over time. Despite prior reports of improved progression‐free survival and overall survival of patients with pseudolymphomatous angiosarcoma, this patient showed rapid disease progression.
Where and why do conifer forests persist in refugia through multiple fire events?
Authors: Downing William M. , Meigs Garrett W. , Gregory Matthew J. , Krawchuk Meg A. 
Published: April 2021

AbstractChanging wildfire regimes are causing rapid shifts in forests worldwide. In particular, forested landscapes that burn repeatedly in relatively quick succession may be at risk of conversion when pre‐fire vegetation cannot recover between fires. Fire refugia (areas that burn less frequently or severely than the surrounding landscape) support post‐fire ecosystem recovery and the persistence of vulnerable species in fire‐prone landscapes. Observed and projected fire‐induced forest losses highlight the need to understand where and why forests persist in refugia through multiple fires. This research need is particularly acute in the Klamath‐Siskiyou ecoregion of southwest Oregon and northwest California, USA, where expected increases in fire activity and climate warming may result in the loss of up to one‐third of the region's conifer forests, which are the most diverse in western North America. Here, we leverage recent advances in fire progression mapping and weather interpolation, in conjunction with a novel application of satellite smoke imagery, to model the key controls on fire refugia occurrence and persistence through one, two, and three fire events over a 32‐year period. Hotter‐than‐average fire weather was associated with lower refugia probability and higher fire severity. Refugia that persisted through three fire events appeared to be partially entrained by landscape features that offered protection from fire, suggesting that topographic variability may be an important stabilizing factor as forests pass through successive fire filters. In addition, smoke density strongly influenced fire effects, with fire refugia more likely to occur when smoke was moderate or dense in the morning, a relationship attributable to reduced incoming solar radiation resulting from smoke shading. Results from this study could inform management strategies designed to protect fire‐resistant portions of biologically and topographically diverse landscapes.
A prepared platelet‐rich plasma extract, namely Self‐Growth Colony, inhibits melanogenesis by down‐regulating microphthalmia‐associated transcription factor in skin melanocyte
Authors: Guo Maggie Suisui , Wu Qiyun , Lai Queenie Wing Sze , Wang Xiaoyang , Bai Panzhu , Fung Kelly Wing Chi , Dong Tina Tingxia , Tsim Karl Wah Keung 
Published: April 2021

AbstractBackgroundDuring melanogenesis, melanocytes produce melanin through enzymatic reactions. Microphthalmia‐associated transcription factor (MITF) is a major regulator in controlling the expressions of melanogenic enzymes tyrosinase (TYR), tyrosine‐related protein‐1 (TRP1), and dopachrome tautomerase (DCT). Self‐Growth Colony (SGC) is prepared from human platelet‐rich plasma (PRP) having an enrichment of growth factors, and which has claimed skin regeneration function.AimIn this study, we aim to identify and investigate the novel role of SGC in skin melanogenesis.MethodsMTT assay was performed to determine the cytotoxicity of applied SGC. Melanin assay was adopted to quantify the intracellular melanin after SGC treatment. Promoter‐driven luciferase assay, real‐time PCR, and Western blotting were performed to determine the expressions of melanogenic enzymes and MITF in SGC‐treated cultured Melan‐A cells, being treated with or without UV induction. Ex vivo mouse skin was treated with SGC, and then was subjected to Western blotting and histochemical staining.ResultsWe identified that SGC inhibited melanogenesis in cultured melanocytes and ex vivo mouse skin. The phenomena were attributed to a reduction of MITF expression, which subsequently down‐regulated the melanogenic enzymes, that is, TYR, TRP1, and DCT. Moreover, ERK signaling was activated in the SGC‐inhibited melanogenesis.ConclusionsThe findings suggest that SGC extracting from human blood can be a safe and potential agent in promoting skin whitening.
Structured simulations improves students’ knowledge acquisition and perceptions of teaching effectiveness: A quasi‐experimental study
Authors: Taha Asma A. , Jadalla Ahlam , Bin Ali Wafaa , Firkins Jenny , Norman Sharon , Azar Najood 
Published: April 2021

AbstractAimsTo determine the effect of adding structured simulation to a traditional classroom lecture format on students’ knowledge acquisition and their evaluation of faculty teaching effectiveness, compared to traditional classroom lectures alone.BackgroundThere is a critical lack of high‐quality clinical placements/experiences in nursing education, particularly in clinical specialty populations, such as paediatrics. Simulation has been shown to help students practice in a safe environment. However, less is known about the outcomes of embedding simulation in didactic class sessions or classroom lectures. Additionally, data on the impact of simulation as a teaching pedagogy on faculty teaching effectiveness is limited.DesignPost‐test, nonequivalent control group quasi‐experimental study.MethodsStudents in two prelicensure nursing programs participated in a 10‐week term paediatric nursing course taught by the same faculty member on two different campuses. The students at one campus, designated as the control group (n = 43), received four hours of traditional, lecture‐only, instructions. The group at a second campus, the intervention group (n = 44), received the same lectures with added structured simulations. Students’ knowledge acquisition and their evaluation of faculty teaching effectiveness were measured in both groups using the same standardised assessment measures. The CONSORT checklist was followed.ResultsStudents’ knowledge acquisition scores and their evaluation scores of faculty teaching effectiveness were significantly higher in the intervention (simulation) group compared to the control group. A significantly higher number of students in the simulation group scored above the national average Nursing Care of Children score as compared to students in the control group.ConclusionsIntegrating simulation with didactic instruction enhanced students’ knowledge acquisition and improved their opinion of faculty teaching effectiveness.Relevance to clinical practiceAugmenting lecture with simulation may provide students with learning experiences that they may not have during clinical rotation due to a lack of paediatric clinical placement sites and differences between sites.
Prion protein is associated with a worse prognosis of head and neck squamous cell carcinoma
Authors: Santos Eloa Mangabeira , Fraga Carlos Alberto de Carvalho , Xavier Alessandra Rejane Ericsson de Oliveira , Xavier Mauro Aparecido de Souza , Souza Marcela Gonçalves , Jesus Sabrina Ferreira de , Paula Alfredo Maurício Batista de , Farias Lucyana Conceição , Santos Sérgio Henrique Sousa , Santos Tiago Goss , Beraldo Flavio H. , Guimarães André Luiz Sena 
Published: April 2021

AbstractBackgroundHead and neck squamous cell carcinoma (HNSC) etiopathogenesis remains unclear, and the biological changes with the activation of heat shock proteins (HSPs) and prion protein (PRNP) promoted by hypoxia in HNSC are undetermined. This study investigates hypoxia's effect in lymph node metastasis by PRNP expression changes and its main partners.MethodsThe study combined a theoretical/cell culture study with a case‐control study. First, bioinformatics and cell culture were performed. A case‐control study was performed in a second step by comparing HNSC patients with and without lymph node metastasis.AnalysesThe Cancer Genome Atlas (TCGA) data source validates the theory in the global population study.ResultsBioinformatics analysis suggests that hypoxia‐inducible factor‐1α (HIF1A) is associated with HSPA4, HSP90AA1 and PRNP expression. TCGA data validate the hypothesis that higher HSP90AA1, HSPA4 and PRNP are related to metastases and low survival. Herein, the cell study demonstrated that muted PRNP did not respond to hypoxia.DiscussionOur results collectively provide the first evidence that PRNP promotes HNSC lymph node metastasis progression through the upregulation of HSPA4, HSP90AA1 and HIF1A. Our findings may provide a molecular basis for the promoting Role of PRNP in HNSC progression.