bluuebunny/crossref_metadata_2025_split huggingface dataset:
One score to rule them all: severity assessment in laboratory mice
Authors: Talbot Steven R. , Struve Birgitta , Wassermann Laura , Heider Miriam , Weegh Nora , Knape Tilo , Hofmann Martine C. J. , von Knethen Andreas , Jirkof Paulin , Keubler Lydia , Bleich André , Häger Christine 
Published: June 2020

AbstractAnimal welfare and the refinement of experimental procedures are fundamental aspects of biomedical research. They provide the basis for robust experimental designs and reproducibility of results. In many countries, the determination of welfare is a mandatory legal requirement and implies the assessment of the degree of the severity that an animal experiences during an experiment. However, for an effective severity assessment, an objective and exact approach/system/strategy is needed. In light of these demands, we have developed the Relative Severity Assessment (RELSA) score.This comprehensive composite score was established on the basis of physiological and behavioral data from a surgical mouse study. Body weight, the Mouse Grimace Scale score, burrowing behavior, and the telemetry-derived parameters heart rate, heart rate variability, temperature, and general activity were used to investigate the quality of indicating severity during postoperative recovery. The RELSA scores not only revealed individual severity levels but also allowed a comparison of severity in distinct mouse models addressing colitis, sepsis, and restraint stress using ak-means clustering approach with the maximum achieved RELSA scores.We discriminated and classified data from sepsis nonsurvivors into the highest relative severity level. Data from mice after intraperitoneal transmitter implantation and sepsis survivor al were located in the next lower cluster, while data from mice subjected to colitis and restraint stress were placed in the lowest severity cluster. Analysis of individual variables and their combinations revealed model- and time-dependent contributions to severity levels.In conclusion, we propose the RELSA score as a validated tool for objective real-time applicability in severity assessment and as a first step towards a unified and accessible risk assessment tool in biomedical research. As an effective severity assessment system, it will fundamentally improve animal welfare, as well as data quality and reproducibility.
Revealing grand-paternal programming of lipid metabolism using a novel computational tool
Authors: Furse Samuel , Watkins Adam J. , Chiarugi Davide , Hojat Nima , Smith James , Williams Huw E. L. , Koulman Albert 
Published: June 2020

AbstractWhile the consequences of poor maternal diet on the offspring’s cardio-metabolic health have been studied in detail, the role of the father’s diet on the health of his offspring is poorly understood. We used a known mouse model to establish the impact of an isocaloric paternal low-protein high-carbohydrate diet on the offspring’s lipid metabolism. Detailed lipid profiles were acquired from F1 neonate (3 weeks), F1 adult (16 weeks) and F2 neonate male and female offspring, in serum, liver, brain, heart and abdominal adipose tissues by Mass Spectrometry and Nuclear Magnetic Resonance. Using a purpose-built computational tool for analysing lipid metabolism as a network, we characterised the number, type and abundance of lipid variables in and between tissues (Lipid Traffic Analysis), finding a variety of alterations associated with paternal diet. These elucidate a mechanism for the defective physiological behaviour of systems at risk of cardio-metabolic disease.
Biochemical evidence of furin specificity and potential for phospho-regulation at Spike protein S1/S2 cleavage site in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV
Authors: Örd Mihkel , Faustova Ilona , Loog Mart 
Published: June 2020

AbstractThe Spike protein of the novel coronavirus SARS-CoV2 contains an insertion680SPRRAR↓SV687forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous insertion was present in the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognitionin vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insertSPRRAR↓SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furin’s ability to cleave the site. Although phosphoregulation of secreted proteins is still poorly understood, further studies, supported by a recent report of tenin vivophosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.
Deconstructing glucose-mediated catabolite repression of thelacoperon ofEscherichia coli: II. Positive feedback exists and drives the repression
Authors: Aggarwal Ritesh K. , Narang Atul 
Published: June 2020

AbstractThe expression of thelacoperon ofE. coliis subject to positive feedback during growth in the presence of gratuitous inducers, but its existence in the presence of lactose remains controversial. The key question in this debate is: Do the lactose enzymes, Lac permease and β-galactosidase, promote accumulation of allolactose? If so, positive feedback exists since allolactose does stimulate synthesis of the lactose enzymes. Here, we addressed the above question by developing methods for determining the intracellular allolactose concentration as well as the kinetics of enzyme induction and dilution. We show that duringlacinduction in the presence of lactose, the intracellular allolactose concentration increases with the lactose enzyme level, which implies that lactose enzymes promote allolactose accumulation, and positive feedback exists. We also show that duringlacrepression in the presence of lactose + glucose, the intracellular allolactose concentration decreases with the lactose enzyme levels, which suggests that under these conditions, the positive feedback loop turns in the reverse direction. The induction and dilution rates derived from the transient data show that the positive feedback loop is reversed due to a radical shift of the steady state induction level. This is formally identical to the mechanism driving catabolite repression in the presence of TMG + glucose.
Regulation of the activity of an antimicrobial peptide by sterols or hopanoids: possible role in cell recognition
Authors: Alvares Dayane S. , Monti Mariela R. , Neto João Ruggiero , Wilke Natalia 
Published: June 2020

AbstractIt is now accepted that hopanoids act as sterol-surrogates in membranes of some sterol-lacking bacteria. Here we inquiry whether the hopanoid diplopterol (DP) could attenuate the activity of the antimicrobial peptide Polybia-MP1 (MP1) similarly to cholesterol (CHO). Survival ofP. aeruginosaexposed to MP1 was lower for cells incubated with DP than those incubated with CHO, and the affinity and subsequent effect of the peptide on lipid bilayers were different in the presence of DP than in the presence of CHO. Membrane properties showed a non-monotonic behavior as the peptide adsorbed, penetrated, and translocated bilayers with DP suggesting a reorganization of MP1 during these processes. We conclude that MP1 selectivity is finely tuned by lipid composition, and propose the differential interaction and consequent effect promoted by the peptide in membranes with diplopterol as a promising starting point for targeting antimicrobial peptides to hopanoid-containing bacterial membranes.
Predicting lapses of attention with sleep-like slow waves
Authors: Andrillon Thomas , Burns Angus , MacKay Teigane , Windt Jennifer , Tsuchiya Naotsugu 
Published: June 2020

AbstractAttentional lapses are ubiquitous and can negatively impact performance. They correlate with mind wandering, or thoughts that are unrelated to ongoing tasks and environmental demands. In other cases, the stream of consciousness itself comes to a halt and the mind goes blank. What is happening in the brain that leads to these mental states? To understand the neural mechanisms underlying attentional lapses, we cross-analysed the behaviour, subjective experience and neural activity of healthy participants performing a task. Random interruptions prompted participants to indicate their mental states as task-focused, mind-wandering or mind-blanking. High-density electroencephalography revealed the occurrence of spatially and temporally localized slow waves, a pattern of neural activity characteristic of the transition toward sleep. These slow waves accompanied behavioural markers of lapses and preceded reports of mind wandering and mind blanking. Furthermore, the location of slow waves distinguished sluggish versus impulsive behaviours, mind wandering versus mind blanking. Our results suggest attentional lapses share a common physiological origin: the emergence of local sleep-like activity within the awake brain.
RAAS blockade, kidney disease, and expression ofACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells
Authors: Subramanian Ayshwarya , Vernon Katherine A , Slyper Michal , Waldman Julia , Luecken Malte D , Gosik Kirk , Dubinsky Dan , Cuoco Michael S , Keller Keith , Purnell Jason , Nguyen Lan , Dionne Danielle , Rozenblatt-Rosen Orit , Weins Astrid ,   Human Cell Atlas Lung Biological Network, Regev Aviv , Greka Anna 
Published: June 2020

AbstractSARS-CoV-2, the coronavirus that causes COVID-19, binds to angiotensin-converting enzyme 2 (ACE2) on human cells. Beyond the lung, COVID-19 impacts diverse tissues including the kidney. ACE2 is a key member of the Renin-Angiotensin-Aldosterone System (RAAS) which regulates blood pressure, largely through its effects on the kidney. RAAS blockers such as ACE inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs) are widely used therapies for hypertension, cardiovascular and chronic kidney diseases, and therefore, there is intense interest in their effect on ACE2 expression and its implications for SARS-CoV-2 pathogenicity. Here, we analyzed single-cell and single-nucleus RNA-seq of human kidney to interrogate the association of ACEi/ARB use withACE2expression in specific cell types. First, we performed an integrated analysis aggregating 176,421 cells across 49 donors, 8 studies and 8 centers, and adjusting for sex, age, donor and center effects, to assess the relationship ofACE2with age and sex at baseline. We observed a statistically significant increase inACE2expression in tubular epithelial cells of the thin loop of Henle (tLoH) in males relative to females at younger ages, the trend reversing, and losing significance with older ages.ACE2expression in tLoH increases with age in females, with an opposite, weak effect in males. In an independent cohort, we detected a statistically significant increase inACE2expression with ACEi/ARB use in epithelial cells of the proximal tubule and thick ascending limb, and endothelial cells, but the association was confounded in this small cohort by the underlying disease. Our study illuminates the dynamics ofACE2expression in specific kidney cells, with implications for SARS-CoV-2 entry and pathogenicity.
Constraints on the Efficiency of Electromicrobial Production
Authors: Salimijazi Farshid , Kim Jaehwan , Schmitz Alexa , Grenville Richard , Bocarsly Andrew , Barstow Buz 
Published: June 2020

AbstractElectromicrobial production technologies (EMP) aim to combine renewable electricity and microbial metabolism. We have constructed molecular to reactor scale models of EMP systems using H2-oxidation and extracellular electron transfer (EET). We predict the electrical-to-biofuel conversion efficiency could rise to ≥ 52% with in vivo CO2-fixation. H2 and EET-mediated EMP both need reactors with high surface areas. H2-diffusion at ambient pressure requires areas 20 to 2,000 times that of the solar photovoltaic (PV) supplying the system. Agitation can reduce this to less than the PV area, and the power needed becomes negligible when storing ≥ 1.1 megawatts. EET-mediated systems can be built that are ≤ 10 times the PV area and have minimal resistive energy losses if a conductive extracellular matrix (ECM) with a resistivity and height seen in natural conductive biofilms is used. The system area can be reduced to less than the PV area if the ECM conductivity and height are increased to those of conductive artificial polymers. Schemes that use electrochemical CO2-fixation could achieve electrical-to-fuel efficiencies of almost 50% with no complications of O2-sensitivity.
The buds ofOscarella lobularis(Porifera): a new convenient model for sponge cell and developmental biology
Authors: Caroline Rocher , Amélie Vernale , Laura Fierro-Constaín , Nina Séjourné , Sandrine Chenesseau , Christian Marschal , Emilie Le Goff , Morgan Dutilleul , Cédric Matthews , Florent Marschal , Nicolas Brouilly , Dominique Massey-Harroche , Alexander Ereskovsky , André Le Bivic , Carole Borchiellini , Emmanuelle Renard 
Published: June 2020

AbstractThe comparative study of the four non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, Porifera) should provide insights into the origin of bilaterian traits. Except for Cnidaria, present knowledge on the cell biology and development of these animals is so far limited. Non-bilaterian models are needed to get further into cell architecture and molecular mechanisms.Given the developmental, histological, ecological and genomic differences between the four sponge classes, we develop a new sponge model: the buds of theOscarella lobularis(class Homoscleromorpha). This experimental model supplements the two other most famous sponge modelsAmphimedon queenslandicaandEphydatia muelleri, both belonging to the class Demospongiae.Budding is a natural and spontaneous asexual reproduction mean, but budding can be triggeredin vitroensuring availability of biological material all year long. We provide a full description of buds, from their formation to their development into juveniles. Their transparency enables fluorescent and live imaging, and their abundance allows for experimental replicates. Moreover, regeneration and cell reaggregation capabilities provide interesting experimental morphogenetic contexts. The numerous techniques now mastered on these buds make it a new suitable sponge model.Summary statementStudying sponge biology is needed to understand the evolution of metazoans. We developed a new model suitable for experimental biology that allows to study morphogenetic processes with modern tools.
Sphingosine 1-phosphate activates the MAP3K1-JNK pathway to promote epithelial movement and morphogenesis
Authors: Wang Jingjing , Mongan Maureen , Chun Jerold , Xia Ying 
Published: June 2020

AbstractMAP 3 kinase 1 (MAP3K1) plays an essential role in embryonic eyelid development. It regulates epithelial morphogenesis through the spatial-temporal activation of Jun N-terminal kinases (JNKs), resulting in forward progression of the embryonic eyelid epithelial cells to enable eyelid closure. The developmental signals that activate the MAP3K1-JNK pathway are still unknown, mainly due to the lack of suitable keratinocyte lines to elucidate the mechanisms of pathway regulation. To address this deficiency, we developed a straightforward method for long-term culture of mouse keratinocytes in feeder-free conditions using Ca2+-free media. Cells grown under these conditions displayed characteristic basal epithelial morphology and keratin 14 expression, but did not form tight- or adherens-junctions. Increased extracellular Ca2+levels restored the formation of cell-cell junctions. Using keratinocyte lines derived from wild type andMap3k1-deficient mice, we found that sphingosine 1-phosphate (S1P) activated the JNK-c-JUN pathways in a manner dependent on MAP3K1 kinase activity and that this MAP3K1-mediated signaling led to epithelial cell migration. Thein vivoroles of this pathway were examined through crossing of genetic mutant mice. Loss-of-function of the S1P receptor(S1pr) 2/3 became haploinsufficient only when combined withMap3k1andJnk1mutations such that the compound mutants displayed eyelid closure defects, suggesting these gene products cooperated in eye morphogenesis. Results of this work establish the S1PR-MAP3K1-JNK pathway as a crucial signaling mechanism for epithelial cell movement and morphogenesis.
Two classes of active transcription sites and their roles in developmental regulation
Authors: Robinson-Thiewes Sarah , McCloskey John , Kimble Judith 
Published: June 2020

AbstractGenes encoding powerful developmental regulators are exquisitely controlled, often at multiple levels. Here, we use single molecule FISH (smFISH) to investigate nuclear active transcription sites (ATS) and cytoplasmic mRNAs of three key regulatory genes along theC. elegans germline developmental axis. The genes encode ERK/MAP kinase and core components of the Notch-dependent transcription complex. Using differentially-labeled probes spanning either a long first intron or downstream exons, we identify two ATS classes that differ in transcriptional progression: iATS harbor partial nascent transcripts while cATS harbor full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis in a gene-, stage- and sex-specific manner. Moreover, regions with more frequent iATS make fewer full-length nascent transcripts and mRNAs, whereas those with more frequent cATS produce more of them. We propose that the regulated balance of these two ATS classes has a major impact on transcriptional output during development.
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions
Authors: Zarin Taraneh , Strome Bob , Peng Gang , Pritišanac Iva , Forman-Kay Julie D , Moses Alan M 
Published: June 2020

AbstractPreviously, we showed that intrinsically disordered regions in proteins (IDRs) contain multiple sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al. 2019). Here, we aim to use these molecular features to make specific functional predictions for individual IDRs and identify the molecular features within them that are responsible for specific functions. We find that the predictable functions are diverse, identifying previously known associated molecular features, as well as features that were previously not known to be associated with these functions. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.
Recalcitrance ofCannabis sativatode novoregeneration; a multi-genotype replication study
Authors: Monthony Adrian S. , Kyne Sean T. , Grainger Christopher M. , Jones A. Maxwell P. 
Published: June 2020

1AbstractCannabis sativais relatively recalcitrant to regeneration from somatic tissues, but several reports have been published demonstrating a response. Most reports show low levels of regeneration from somatic tissues, but a landmark publication by Lataet al. in 2010 reported regeneration from leaf explants with a 96% response rate, producing an average of 12.3 shoots per explant in a single, high-THC genotype. Despite the importance regeneration plays in plant biotechnology this protocol has not been used in subsequent papers in the decade since it was published, raising the concern that it is not reproducible. Many researchers are looking to build research programmes in this growing field, and it is important that the reproducibility and robustness of single-genotypeC. sativaregeneration protocols undergo multi-lab validations to ensure they are reproducible across the species. Replication studies in this burgeoning field will help research groups avoid lost time and resources which arise from pursuing protocols that are not reproducible. Here we test the replicability of this protocol across 10 drug-typeC. sativagenotypes. This protocol successfully induced callus in all 10 genotypes. Callus size and appearance substantially differed among cultivars, with the most responsive genotype producing 6-fold more callus than the least responsive genotype. However, the most successful shoot induction medium developed in the 2010 paper failed to induce regeneration in any of the cultivars tested, resulting in the eventual necrosis of the calli. Based on this replication study, it is evident that the existing regeneration protocol is not robust and could not be replicated in any of the 10 genotypes tested.
Parabrachial Opioidergic Projections to Preoptic Hypothalamus Mediate Behavioral and Physiological Thermal Defenses
Authors: Norris Aaron J. , Shaker Jordan R. , Cone Aaron L. , Ndiokho Imeh B. , Bruchas Michael R 
Published: June 2020

SummaryMaintaining stable body temperature through environmental thermal stressors requires detection of temperature changes, relay of information, and coordination of physiological and behavioral responses. Studies have implicated areas in the preoptic hypothalamic area (POA) and the parabrachial nucleus (PBN) as nodes in the thermosensory neural circuitry and indicate the opioid system within the POA is vital in regulating body temperate. In the present study we identify neurons projecting to the POA from PBN expressing the opioid peptides Dynorphin (Dyn) and Enkephalin (Enk). We determine that warm-activated PBN neuronal populations overlap with both Dyn and Enk expressing PBN populations. We demonstrate that Dyn and Enk expressing neurons are partially overlapping subsets of a glutamatergic population in the PBN. Using optogenetic approaches we selectively activate projections in the POA from PBN Dyn, Enk, and VGLUT2 expressing neurons. Our findings demonstrate that Dyn, Enk, and VGLUT2 expressing PBN neurons are critical for physiological and behavioral heat defense.
A Live-Cell Assay for the Detection of pre-microRNA-Protein Interactions
Authors: Rosenblum Sydney L. , Lorenz Daniel A. , Garner Amanda L. 
Published: June 2020

AbstractRecent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of both coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, we have devised a conceptually new assay for the live-cell detection of RNA-protein interactions (RPIs), RNA interaction with Protein-mediated Complementation Assay, or RiPCA. As proof-of-concept, we have utilized the interaction of the pre-microRNA, pre-let-7, with its binding partner, Lin28. Using this system, we have demonstrated the selective detection of the pre-let-7-Lin28 RPI in both the cytoplasm and nucleus. Furthermore, we determined this technology can be used to discern relative affinities for specific sequences as well as of individual RNA binding domains. Thus, RiPCA has the potential to serve as a useful tool in supporting the investigation of cellular RPIs.