bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epithelial Regeneration Ability of Crohn’s Disease Assessed Using Patient-Derived Intestinal Organoids
Authors: Lee Chnasu , Hong Sung Noh , Kim Eun Ran , Chang Dong Kyung , Kim Young-Ho 
Published: March 2021

AbstractBackgroundThe intrinsic limitation of cell lines and animal models limits our understanding of epithelial regeneration capability in Crohn’s disease (CD). Therefore, we aimed to study epithelial regeneration ability in CD using an intestinal organoid model. Further, since tumor necrosis factor alpha (TNFα) is a major proinflammatory effector during CD pathogenesis, we also investigated TNFα-induced alteration of regeneration ability in CD patient-derived intestinal organoids.MethodsHuman intestinal organoids were constructed in a three-dimensional intestinal crypt culture of enteroscopic biopsy samples from control subjects and patients with CD. The epithelial regeneration ability of intestinal organoids was assessed using organoid reconstitution, 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2′-deoxyuridine (EdU), and wound healing assays.ResultsEx vivocultures of ileal crypt cells revealed that organoid formation rate of CD patients were reduced compared with that of control subjects (p<.001). CD patient-derived organoids sub-cultured for more than 6 passages showed stable organoid reconstitution and identical morphological features. The organoid constitution and MTT assay revealed that the viability of TNFα-treated CD patient-derived organoids were significantly lower than that of TNFα-treated control organoids (p<.05 for each). The number of EdU+ proliferative cells was significantly lower in TNFα-treated CD patient-derived organoids than in TNFα-treated control organoids (p<.05). The wound-healing ability of TNFα-treated CD patient-derived organoids was significantly lower than that of TNFα-treated control organoids (p<.001).ConclusionsThe clinical trials are disabled to settle this issue, our results indicated that the epithelial regenerative ability is impaired in patients with CD, especially in TNFα-enriched condition.
Association of Urine Findings with Metabolic Syndrome Traits in a Population of Patients with Nephrolithiasis
Authors: Hood Virginia L. , Sternberg Kevan M. , de Waal Desiree , Asplin John R. , Mulligan Carley , Callas Peter W. 
Published: March 2021

AbstractBackground and objectivesThe odds of nephrolithiasis increase with more metabolic syndrome (met-s) traits. We evaluated associations of metabolic and dietary factors from urine studies and stone composition with met-s traits in a large cohort of stone-forming patients.Design, setting, participants & measurementsPatients >18 years, who were evaluated for stones with 24 h urine collections, July 2009-December 2018, had records reviewed retrospectively. Patient factors, laboratory values and diagnoses were identified within 6 months of urine collection and stone composition within 1 year. Four groups with 0, 1, 2, ≥ 3 met-s traits (hypertension, obesity, dyslipidemia, diabetes) were evaluated. Trends across groups were tested using linear contrasts in analysis of variance and analysis of covariance.Results1473 patients met inclusion criteria (835 with stone composition). Met-s groups were 0=684, 1=425, 2=211, 3 and 4 =153. There were no differences among groups for urine volume, calcium or ammonium (NH4) excretion. There was a significant trend (p<0.001) for more met-s traits being associated with decreasing urine pH, increasing age, calculated dietary protein, urine uric acid, oxalate, citrate, titratable acid (TAP), net acid excretion (eNAE) and uric acid supersaturation. The ratio of ammonium to net acid excretion did not differ among the groups.After adjustment for protein intake, the fall in urine pH remained strong, while the upward trend in TAP excretion was attenuated and NH4 decreased. Calcium oxalate stones were most common, but there was a trend for more uric acid (p<0.001) and fewer calcium phosphate (p=0.09) and calcium oxalate stones (p=0.01) with more met-s traits.ConclusionsStone forming patients with met-s have a defined pattern of metabolic and dietary risk factors that contribute to an increased risk of stone formation including higher acid excretion, largely the result of higher protein intake, and lower urine pH.
P2X2 receptor subunit interfaces are missense variant hotspots where mutations tend to increase apparent ATP affinity
Authors: Gasparri Federica , Sarkar Debayan , Bielickaite Sarune , Poulsen Mette Homann , Hauser Alexander Sebastian , Pless Stephan Alexander 
Published: March 2021

ABSTRACTBackground and PurposeP2X receptors (P2XRs) are trimeric ligand-gated ion channels (LGICs) that open a cation-selective pore in response to ATP binding to their large extracellular domain (ECD). The seven known P2XR subtypes can assemble as homo- or heterotrimeric complexes and contribute to numerous physiological functions, including nociception, inflammation and hearing. The overall structure of P2XRs is well established, but little is known about the spectrum and prevalence of human genetic variations and the functional implications in specific domains.Experimental ApproachHere we examine the impact of P2X2 receptor (P2X2R) inter-subunit interface missense variants identified in the human population or through structural predictions. We test both single and double mutants through electrophysiological and biochemical approaches.Key resultsWe demonstrate that predicted ECD inter-subunit interfaces display a higher-than-expected density of missense variations and that the majority of mutations that disrupt putative inter-subunit interactions result in channels with higher apparent ATP affinity. Lastly, we show that double mutants at the subunit interface show significant energetic coupling, especially if located in close proximity.Conclusions and ImplicationsWe provide the first structural mapping of the mutational burden across the human population in a LGIC and show that the density of missense mutations is constrained between protein domains, indicating evolutionary selection at the domain level. Our data may indicate that, unlike other LGICs, P2X2Rs have evolved an intrinsically high threshold for activation, possibly to allow for additional modulation or as a cellular protection mechanism against overstimulation.Bullet point summary‘What is already known’:P2X2 receptors are ATP-activated ion channels implicated in hearing and nociceptice pathways‘What this study adds’:A structural mapping of missense variants observed in the human populationWe identify the intersubunit-interface as a variant hotspot and decipher functional impact of mutations‘Clinical significance’:The development of both inhibitors and activators of P2X2 receptor function may be required
The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications inVibrio natriegens
Authors: Stukenberg Daniel , Hensel Tobias , Hoff Josef , Daniel Benjamin , Inckemann René , Tedeschi Jamie N. , Nousch Franziska , Fritz Georg 
Published: March 2021

AbstractVibrio natriegensis known as the world’s fastest growing organism with a doubling time of less than 10 minutes. This incredible growth speed empowersV. natriegensas a chassis for synthetic and molecular biology, potentially replacingE. coliin many applications. While first genetic parts have been built and tested forV. natriegens, a comprehensive toolkit containing well-characterized and standardized parts did not exist. To close this gap, we created the Marburg Collection – a highly flexible Golden Gate Assembly-based cloning toolbox optimized for the emerging chassis organismV. natriegens. The Marburg Collection overcomes the paradigm of plasmid construction – integrating inserts into a backbone – by enabling thede novoassembly of plasmids from basic genetic parts. This allows users to select the plasmid replication origin and resistance part independently, which is highly advantageous when limited knowledge about the behavior of those parts in the target organism is available. Additional design highlights of the Marburg Collection are novel connector parts, which facilitate modular circuit assembly and, optionally, the inversion of individual transcription units to reduce transcriptional crosstalk in multigene constructs. To quantitatively characterize the genetic parts contained in the Marburg Collection inV. natriegens, we developed a reliable microplate reader measurement workflow for reporter experiments and overcame organismspecific challenges. We think the Marburg Collection with its thoroughly characterized parts will provide a valuable resource for the growingV. natriegenscommunity.
Inferring cell cycle phases from a partially temporal network of protein interactions
Authors: Lucas Maxime , Morris Arthur , Townsend-Teague Alex , Tichit Laurent , Habermann Bianca H. , Barrat Alain 
Published: March 2021

AbstractThe temporal organisation of biological systems into phases and subphases is often crucial to their functioning. Identifying this multiscale organisation can yield insight into the underlying biological mechanisms at play. To date, however, this identification requiresa prioribiological knowledge of the system under study. Here, we recover the temporal organisation of the cell cycle of budding yeast into phases and subphases, in an automated way. To do so, we model the cell cycle as a partially temporal network of protein-protein interactions (PPIs) by combining a traditional static PPI network with protein concentration or RNA expression time series data. Then, we cluster the snapshots of this temporal network to infer phases, which show good agreement with our biological knowledge of the cell cycle. We systematically test the robustness of the approach and investigate the effect of having only partial temporal information. Our results show for the first time that a temporal network with only partial temporal information, i.e. for some of the PPIs, is sufficient to infer the temporal organization of a system. The generality of the method makes it suitable for application to other, less well-known biological systems for which the temporal organisation of processes plays an important role.
D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1
Authors: Gupta Suchetana , Mallick Ditipriya , Banerjee Kumarjeet , Mukherjee Shrimon , Sarkar Soumyadev , Lee Sonny TM , Basuchowdhuri Partha , Jana Siddhartha S 
Published: March 2021

AbstractThe clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, contribution of the mutations in each of the viral genes towards the degree of severity needs a deeper understanding for designing a better therapeutic approach against COVID-19. Open Reading Frame-3a (ORF3a) protein has been found to be mutated at several positions. In this work, we have studied the effect of one of the most frequently occurring mutants, D155Y of ORF3a protein, found in Indian COVID-19 patients. Using computational simulations we demonstrated that the substitution at 155th changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein compared with the other substitutions found in Indian patients. Protein-protein docking using HADDOCK analysis revealed that substitution D155Y weakened the binding affinity of ORF3a with caveolin-1 compared with the other substitutions, suggesting its importance in the overall stability of ORF3a-caveolin-1 complex, which may modulate the virulence property of SARS-CoV-2.
Overabundance ofAsaiaandSerratiabacteria is associated with deltamethrin insecticide susceptibility inAnopheles coluzziifrom Agboville, Côte d’Ivoire
Authors: Pelloquin Bethanie , Kristan Mojca , Edi Constant , Meiwald Anne , Clark Emma , Jeffries Claire L. , Walker Thomas , Dada Nsa , Messenger Louisa A. 
Published: March 2021

AbstractBackgroundInsecticide resistance among mosquito species is now a pervasive phenomenon, which threatens to jeopardise global malaria vector control efforts. Evidence of links between the mosquito microbiota and insecticide resistance is emerging, with significant enrichment of insecticide degrading bacteria and enzymes in resistant populations. Using 16S rRNA amplicon sequencing, we characterised and compared the microbiota ofAnopheles(An.)coluzziiin relation to their deltamethrin resistance and exposure profiles.ResultsComparisons between 2-3 day old deltamethrin resistant and susceptible mosquitoes, demonstrated significant differences in microbiota diversity (PERMANOVA, pseudo-F = 19.44, p=0.0015).Ochrobactrum, LysinibacillusandStenotrophomonasgenera, each of which comprised insecticide degrading species, were significantly enriched in resistant mosquitoes. Susceptible mosquitoes had a significant reduction in alpha diversity compared to resistant individuals (Shannon index: H=13.91, q=0.0003, Faith’s phylogenetic diversity: H=6.68, q=0.01), withAsaiaandSerratiadominating microbial profiles. There was no significant difference in deltamethrin exposed and unexposed 5-6 day old individuals, suggesting that insecticide exposure had minimal impact on microbial composition.SerratiaandAsaiawere also dominant in 5-6 day old mosquitoes, regardless of exposure or phenotype, and had reduced microbial diversity compared with 2-3 day old mosquitoes.ConclusionsOur findings revealed significant alterations ofAn. coluzziimicrobiota associated with deltamethrin resistance, highlighting the potential for identification of novel microbial markers for insecticide resistance surveillance. qPCR detection ofSerratiaandAsaiawas consistent with 16S rRNA sequencing, suggesting that population level field screening of the bacterial microbiota may be feasibly integrated into wider resistance monitoring if reliable and reproducible markers associated with phenotype can be identified.
Purkinje Cell Activity in Medial and Lateral Cerebellum During Suppression of Voluntary Eye Movements in Rhesus Macaques
Authors: Avila Eric , Flierman Nico A. , Holland Peter J. , Roelfsema Pieter R. , Frens Maarten A. , Badura Aleksandra , De Zeeuw Chris I. 
Published: March 2021

AbstractVolitional suppression of responses to distracting external stimuli enables us to achieve our goals. This volitional inhibition of a specific behavior is supposed to be mainly mediated by the cerebral cortex. However, recent evidence supports the involvement of the cerebellum in this process. It is currently not known whether different parts of the cerebellar cortex play differential or synergistic roles in planning and execution of this behavior. Here, we measured Purkinje cell (PC) responses in the medial and lateral cerebellum in two rhesus macaques during a pro- and antisaccade task. During an antisaccade trial, non-human primates were instructed to make a saccadic eye movement away from a target, rather than towards it, as in prosaccade trials. Our data shows that the cerebellum plays an important role not only during execution of the saccades, but also during the volitional inhibition of eye movements towards the target. Simple Spike (SS) modulation during the instruction and execution period of pro- and antisaccades was prominent in PCs of both medial and lateral cerebellum. However, only the SS activity in the lateral cerebellar cortex contained information about trial identity and showed a stronger reciprocal interaction with complex spikes. Moreover, SS activity of different PC groups modulated bidirectionally in both regions, but the PCs that showed facilitating and suppressive activity were predominantly associated with instruction and execution, respectively. These findings show that different cerebellar regions and PC groups contribute to goal-directed behavior and volitional inhibition, but with different propensities, highlighting the rich repertoire of cerebellar control in executive functions.Significance StatementThe antisaccade task is commonly used in research and clinical evaluation as a test of volitional and flexible control of behavior. It requires volitional suppression of prosaccades, a function that has been attributed to the neocortex. However, recent findings indicate that cerebellum also contributes to this behavior. We recorded from neurons in the medial and lateral cerebellum to evaluate their responses in this task. We found that both regions significantly modulated their activity during this task, but only cells in the lateral cerebellum encoded the stimulus identity in each trial. These results indicate that the cerebellum actively contributes to the control of flexible behavior and that lateral and medial cerebellum play different roles during volitional eye movements.
TNFAIP8 is a novel phosphoinositide-binding inhibitory regulator of Rho GTPases that promotes cancer cell migration
Authors: Lin Mei , Sun Honghong , Fayngerts Svetlana A. , Huangyang Peiwei , Chen Youhai H. 
Published: March 2021

SUMMARYMore than half of human tumors exhibit aberrantly dysregulated phosphoinositide signaling, yet how this is controlled remains not fully understood. While somatic mutations of PI3K, PTEN and Ras account for many cases of the hyperactivated lipid signals, other mechanisms for these dysfunctions in cancer are also being discovered. We report here that TNFAIP8 interacts with PtdIns(4,5)P2and PtdIns(3,4,5)P3and is likely to be hijacked by cancer cells to facilitate directional migration during malignant transformation. TNFAIP8 maintains the quiescent cellular state by sequestering inactive Rho GTPases in the cytosolic pool, which can be set free upon chemoattractant activation at the leading edge. Consequently, loss of TNFAIP8 results in severe defects of chemotaxis and adhesion. Thus, TNFAIP8, whose expression can be induced by inflammatory cytokines such as TNFαfrom tumor microenvironment, represents a molecular bridge from inflammation to cancer by linking NF-κB pathway to phosphoinositide signaling. Our study on the conserved hydrophobic cavity structure will also advisein silicodrug screening and development of new TNFAIP8-based strategies to combat malignant human diseases.
Metagenomic insight into the plant growth-promoting potential of a diesel-degrading bacterial consortium for enhanced rhizoremediation application
Authors: Eze Michael O. , Thiel Volker , Hose Grant C. , George Simon C. , Daniel Rolf 
Published: March 2021

AbstractThe slow rate of natural attenuation of organic pollutants, together with unwanted environmental impacts of traditional remediation strategies, has necessitated the exploration of plant-microbe systems for enhanced bioremediation applications. The identification of microorganisms capable of promoting both plant growth and hydrocarbon degradation is crucial to the success of plant-based remediation techniques. Through successive enrichments of a soil sample from a historic oil-contaminated site in Wietze, Germany, we isolated a plant growth-promoting and hydrocarbon-degrading bacterial consortium. Metagenome analysis of the consortium led to the identification of genes and taxa putatively associated with these processes. The majority of the coding DNA sequences involved in these reactions were affiliated toAcidocella aminolyticaandAcidobacterium capsulatum.In microcosm experiments performed in association withMedicago sativaL., the consortium achieved 91% rhizodegradation of diesel fuel hydrocarbons within 60 days, indicating its potential for biotechnological applications in the remediation of sites contaminated by organic pollutants.
Bacterial small RNAs and host epigenetic effectors of a transgenerational memory of pathogens inC. elegans
Authors: Legüe Marcela , Aguila Blanca , Pollak Bernardo , Calixto Andrea 
Published: March 2021

AbstractThe inheritance of memories is adaptive for survival. Microbes interact with all organisms challenging their immunity and triggering behavioral adaptations. Some of these behaviors induced by bacteria can be inherited although the mechanisms of action are largely unexplored. In this work, we useC. elegansand its bacteria to study the transgenerational RNA dynamics of an interspecies crosstalk leading to a heritable behavior. Heritable responses to bacterial pathogens in the nematode include avoidance and pathogen-induced diapause (PIDF), a state of suspended animation to evade the pathogen threat. We identify a small RNA RsmY, involved in quorum sensing fromP. aeruginosaas required for initiation of PIDF. Histone methyltransferase SET-18/SMYD3 is also needed for PIDF initiation inC. elegans. In contrast, SET-25/EHMT2 is necessary for the maintenance of the memory of pathogen exposure in the transgenerational lineage. This work can be a starting point to understanding microbiome-induced inheritance of acquired traits.
Coping with COVID: pivoting perspectives from teaching a third-year undergraduate financial accounting course
Authors: Morris Richard D. , Dai Lili , De Groote Sander , Holmes Emma , Lau Leonard , Li Chao Kevin , Nguyen Phuc 
Published: March 2021

Purpose
Coronavirus (COVID-19) has caused upheaval in university teaching practices. This paper aims to document how the teaching team on a large third-year undergraduate financial accounting course in an Australian university coped with the impact of the virus. Changes in teaching practices when classes shifted from face-to-face to online instruction during the COVID-19 crisis are described and examined using the crisis management process framework of Pearson and Clair (1998). Teaching team members were asked to write brief reflections on their experiences teaching the course during the period from February to July 2020. These were then thematically analysed and included as outcomes within the Pearson and Clair (1998) framework.

Design/methodology/approach
Description of COVID-19 induced changes to teaching a large undergraduate financial accounting course at an Australian university.

Findings
Six outcomes emerged: learning new technology; collegiality; the course review; the online delivery experience; redesigning assessments and; time investment; conjectures are offered about the survival of some of the changes made during the year.

Research limitations/implications
The research only covers one teaching team’s experience but that is the purpose of the special issue.

Practical implications
Lessons for the future are explored.

Social implications
The implications of online teaching are explored.

Originality/value
The paper provides a historical record of how the teaching team on a large undergraduate financial accounting course coped with an unexpected, major event that necessitated rapid and radical changes to teaching methods.