bluuebunny/crossref_metadata_2025 huggingface dataset:
Parent Perspectives on Information-seeking, Trustworthiness, and Decision-making in High-risk Neuroblastoma
Authors: Brown Katherine , Benjaminy Shelly , Illes Judy , Deyell Rebecca J.
Published: December 2020

Background:

This study explores how parents of children with high-risk neuroblastoma incorporate information from multiple sources into treatment decision-making for their children as they evaluate the trustworthiness of the sources.

Methods:

Following ethics board approval, parents of children with high-risk neuroblastoma were recruited through purposive sampling from a tertiary care pediatric oncology program in Vancouver, BC, Canada. Participants completed an in-depth, semistructured interview with a study member. The qualitative descriptive methodology was utilized to code interview transcripts and identify emergent themes.

Results:

Nine parents of children with high-risk neuroblastoma during upfront therapy (n=4) or treatment of refractory disease (n=5) were included. Despite almost universal access of web-based information, parents acknowledged distrust in the reliability and consistency of these sources. Open communication between parents and physicians about sources of information outside the clinic and access to regulated, accurate information is highly valued. The impact on the quality of life and the costs, both financial and personal, of travel are key factors in decision-making.

Discussion:

Health care providers shoulder an immense responsibility to augment and contextualize information available about high-risk neuroblastoma for parents to maximize benefit in decision-making. Health care providers should guide access to accurate, evidence-based resources that can be monitored and continuously updated.
Hypoglycemia in a Pediatric Emergency Department
Authors: Papini Laura , Piga Simone , Dionisi-Vici Carlo , Parisi Pasquale , Ciofi degli Atti Marta Luisa , Marcias Michela , Garrone Stefano , Scialanga Barbara , Taurisano Roberta , Reale Antonino , Villa Maria Pia , Raucci Umberto
Published: December 2020

Objectives

This study aimed to establish the rate, etiology, and short-term outcome of hypoglycemia in infants and children accessing an emergency department of a tertiary care pediatric hospital.

Methods

The study was retrospectively conducted on the clinical records of children with hypoglycemia aged 15 days to 17 years who were admitted consecutively to the emergency department during a 6-year period for various clinical conditions. Hypoglycemia was defined as a venous plasma glucose level lower than 45 mg/dL.

Results

Hypoglycemia was detected in 402 patients (female-to-male ratio, 1.26; mean age, 2.6 ± 1.8 years), with a rate of 0.99 per 1000 children. Plasma glucose levels ranged from 3 to 45 (mean, 37.48 ± 7.44) mg/dL. Hypoglycemia was associated with gastroenteritis or other infectious diseases causing protracted fasting in 86.32% of cases, whereas hypoglycemia related to a different etiology (HDE) was observed in 13.68% of hypoglycemic children. Most HDE patients had a final diagnosis of ketotic hypoglycemia, whereas metabolic defects were a rare (1.49%) but nonnegligible etiologic cause. A severe triage code was more frequent in the HDE group (P < 0.001). Factors significantly and independently associated with HDE were impaired level of consciousness, assessed with the AVPU scale (A, alert; V, responding to verbal; P, responding to pain; U, unresponsive; adjusted odds ratio, 2.50; P = 0.025) and clinical onset within 12 hours (adjusted odds ratio, 3.98; P < 0.001).

Conclusions

In a nonnegligible number of critically ill children, hypoglycemia can be detected. In a minority of cases, hypoglycemia was due to metabolic disorders that should be suspected on the basis of the severity of hypoglycemia, and the recent onset and the presence of neuroglycopenic symptoms.
Overview of Breath Testing in Clinical Practice in North America
Authors: Nichols Buford L. , Baker Robert D. , Baker Susan S.
Published: December 2020

Human breath is an easily, noninvasively obtained substance. It offers insight into metabolism and is used to diagnose disaccharide malabsorption, infection, small bowel bacterial over growth, and transit times. Herein, we discuss the readily available clinical breath tests, how they function, how they are administered and interpreted and some pitfalls in their use.
Persistent Primitive Olfactory Artery: Three Cases
Authors: Pendharkar Hima , Bhattacharya Kajari , Yadav Nishtha , Jabeen Shumyla
Published: December 2020

The persistent primitive olfactory artery is a very rare arterial variant with a little over a score of cases reported in literature so far. We present 3 cases illustrating this entity, which were incidentally diagnosed while imaging for other indications.
The Efficacy of Liposomal Bupivacaine on Postoperative Pain Following Abdominal Wall Reconstruction
Authors: Fafaj Aldo , Krpata David M. , Petro Clayton C. , Prabhu Ajita S. , Rosenblatt Steven , Tastaldi Luciano , Alkhatib Hemasat , Tu Chao , Zolin Samuel J. , Thomas Jonah D. , Costanzo Adele M. , Rosen Michael J.
Published: December 2020

Objective:

To study the efficacy of liposomal bupivacaine on postoperative opioid requirement and pain following abdominal wall reconstruction.

Summary Background Data:

Despite the widespread use of liposomal bupivacaine in transversus abdominis plane block, there is inadequate evidence demonstrating its efficacy in open abdominal wall reconstruction. We hypothesized that liposomal bupivacaine plane block would result in decreased opioid requirements compared with placebo in the first 72 hours after surgery.

Methods:

This was a single-center double-blind, placebo-controlled prospective study conducted between July 2018 and November 2019. Adult patients (at least 18 yrs of age) undergoing open, elective, ventral hernia repairs with mesh placed in the retromuscular position were enrolled. Patients were randomized to surgeon-performed transversus abdominis plane block with liposomal bupivacaine, simple bupivacaine, or normal saline (placebo). The main outcome was opioid requirements in the first 72 hours after surgery. Secondary outcomes included total inpatient opioid use, pain scores determined using a 100 mm visual analog scale, length of hospital stay, and patientreported quality of life.

Results:

Of the 164 patients who were included in the analysis, 57 patients received liposomal bupivacaine, 55 patients received simple bupivacaine, and 52 received placebo. There were no differences in the total opioid used in the first 72 hours after surgery as measured by morphine milligram equivalents when liposomal bupivacaine was compared with simple bupivacaine and placebo (325 ± 225 vs 350 ± 284 vs 310 ± 272, respectively,P= 0.725). Similarly, there were no differences in total inpatient opioid use, pain scores, length of stay, and patient-reported quality of life.

Conclusions:

There are no apparent clinical benefits to using liposomal bupivacaine transversus abdominis plane block when compared with simple bupivacaine and placebo for open abdominal wall reconstruction.
Teunia rosae sp. nov. and Teunia rudbeckiae sp. nov. (Cryptococcaceae, Tremellales), two novel basidiomycetous yeast species isolated from flowers
Authors: Wang Gui-Shuang , Zhou Yu , Xue Lu , Li Ai-Hua , Wangmu  , Wang Qi-Ming
Published: December 2020

Three yeast strains isolated from three flower samples were identified as representing two novel species of Teunia based on molecular phylogenetic analysis and phenotypic comparisons. Strains 12A8 and 21S4 with pink cream colonies and subglobose to globose cells had identical sequences in the ITS and LSU D1/D2 regions, which differed from strain X54 with cream colonies and ovoid to ellipsoidal cells by 6 nt substitutions (1 %) and 9 nt mismatches (1.5 %) in the D1/D2 domains and ITS region, respectively. They could also be distinguished from each other in assimilation of glucitol and salicin, growth at 28 °C and cell fibrillar appendages under scanning electron microscopy. The three strains differed from known species of Teunia by more than 8 nt (1.3 %) and 30 nt (5 %) in the D1/D2 domains and ITS region, respectively. Therefore, the names Teunia rudbeckiae sp. nov. (Holotype CGMCC 2.5840, Mycobank MB 835892) and Teunia rosae sp. nov. (Holotype CGMCC 2.5830, MycoBank MB 835891) are proposed to accommodate strain X54, and strains 12A8 and 21S4, respectively.
Perturbation of amygdala-cortical projections reduces ensemble coherence of palatability coding in gustatory cortex
Authors: Lin Jian-You , Mukherjee Narendra , Bernstein Max J. , Katz Donald B.
Published: December 2020

Taste palatability is centrally involved in consumption decisions—we ingest foods that taste good and reject those that don’t. Gustatory cortex (GC) and basolateral amygdala (BLA) almost certainly work together to mediate palatability-driven behavior, but the precise nature of their interplay during taste decision-making is still unknown. To probe this issue, we discretely perturbed (with optogenetics) activity in BLA→GC axons during taste deliveries. This perturbation strongly altered GC taste responses, but while the perturbation itself was tonic (2s), the alterations were not—changes preferentially aligned with the onset times of previously-described taste response epochs, and reduced evidence of palatability-related activity in the “late-epoch” of the responses without reducing the amount of taste identity information available in the “middle epoch.” Finally, BLA→GC perturbations changed behavior-linked taste response dynamics themselves, distinctively diminishing the abruptness of ensemble transitions into the late epoch. These results suggest that BLA “organizes” behavior-related GC taste dynamics.
Osteoprotegerin is elevated in pulmonary fibrosis and associates with IPF progression
Authors: Habibie H. , Putri Kurnia S.S. , Boorsma Carian E. , Brass David M. , Heukels Peter , Wijsenbeek Marlies , Kool Mirjam , van den Berge Maarten , Borghuis Theo , Brandsma Corry-Anke , Gan C Tji , Olinga Peter , Timens Wim , Kahn Nicolas , Kreuter Michael , Burgess Janette K. , Melgert Barbro N.
Published: December 2020

Osteoprotegerin (OPG), a decoy receptor for receptor activator of NF-kB ligand (RANKL), is used as a biomarker for assessing severity of liver fibrosis. However, its expression and role in pulmonary fibrosis are unknown. We hypothesized that OPG also has a role in pulmonary fibrosis.

Human and mouse control and fibrotic lung tissue were used to examine OPG expression, and mouse precision-cut lung slices to study OPG regulation in pulmonary fibrosis. Serum from idiopathic pulmonary fibrosis (IPF) patients and controls was analysed to investigate whether OPG levels correlate with disease status as measured by lung function.

OPG-protein levels were significantly higher in mouse and human fibrotic lung tissue compared to control. OPG-mRNA and protein production were induced in mouse precision-cut-lung slices upon TGFβ stimulation and could be inhibited with galunisertib, a TGFβ receptor kinase inhibitor. OPG-protein levels in fibrotic mouse lung tissue correlated with degree of fibrosis. Isolated lung fibroblasts from IPF patients had higher OPG-protein levels than control fibroblasts. Serum OPG levels in IPF patients, at first presentation, negatively correlated with diffusing capacity to carbon monoxide. Finally, serum OPG levels higher than 1234 pg/ml at first presentation were associated with progression of disease in IPF patients.

In conclusion, OPG is produced in lung tissue, associates with fibrosis, and may be a potential prognostic biomarker for IPF disease progression. Validation in a larger cohort is warranted to further explore the role of OPG in pulmonary fibrosis and its potential for assessing the prognosis of fibrotic lung disease in individual patients.

Take home message

Osteoprotegerin is present in fibrotic lung tissue and high serum levels correlate with low lung function and IPF disease progression in this small study, indicating osteoprotegerin may have value as a biomarker to predict IPF progression
Vectorized Capsid Rendering in the Browser with Capsid.js
Authors: Negrón Daniel Antonio
Published: December 2020

Motivation

Few online services exist for rendering high-quality viral capsid figures compatible with common productivity software to develop effective infographics in the field of virology.

Results

The capsid.js library renders class I viral capsids within an online application that parameterizes style options, perspectives, and lattice patterns with SVG export.

Availability

This project is actively developed on GitHub (https://github.com/dnanto/capsid), distributed under the MIT License, hosted on GitHub Pages, and runs on modern browsers (https://dnanto.github.io/capsid/capsid.html).

Supplementary information

Supplementary data are available on GitHub.
Ultra-high field (7T) functional magnetic resonance imaging in amyotrophic lateral sclerosis: a pilot study
Authors: Barry Robert L. , Babu Suma , Anteraper Sheeba Arnold , Triantafyllou Christina , Keil Boris , Rowe Olivia E. , Rangaprakash D. , Paganoni Sabrina , Lawson Robert , Dheel Christina , Cernasov Paul M. , Rosen Bruce R. , Ratai Eva-Maria , Atassi Nazem
Published: December 2020

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of the central nervous system that results in a progressive loss of motor function and ultimately death. It is critical, yet also challenging, to develop non-invasive biomarkers to identify, localize, measure and/or track biological mechanisms implicated in ALS. Such biomarkers may also provide clues to identify potential molecular targets for future therapeutic trials. Herein we report on a pilot study involving twelve participants with ALS and nine age-matched healthy controls who underwent high-resolution resting state functional magnetic resonance imaging at an ultra-high field of 7 Tesla. A group-level whole-brain analysis revealed a disruption in long-range functional connectivity between the superior sensorimotor cortex (in the precentral gyrus) and bilateral cerebellar lobule VI.Post hocanalyses using atlas-derived left and right cerebellar lobule VI revealed decreased functional connectivity in ALS participants that predominantly mapped to bilateral postcentral and precentral gyri. Cerebellar lobule VI is a transition zone between anterior motor networks and posterior non-motor networks in the cerebellum, and is associated with a wide range of key functions including complex motor and cognitive processing tasks. Our observation of the involvement of cerebellar lobule VI adds to the growing number of studies implicating the cerebellum in ALS. Future avenues of scientific investigation should consider how high-resolution imaging at 7T may be leveraged to visualize differences in functional connectivity disturbances in various genotypes and phenotypes of ALS along the ALS-frontotemporal dementia spectrum.
Loss of SUR1 subtype KATPchannels alters antinociception and locomotor activity after opioid administration
Authors: Sakamaki Gerald , Johnson Kayla , Mensinger Megan , Hmu Eindray , Klein Amanda H.
Published: December 2020

Background

Opioid signaling can occur through several downstream mediators and influence analgesia as well as reward mechanisms in the nervous system. KATPchannels are downstream targets of the μ opioid receptor and contribute to morphine-induced antinociception.

Aims

The aim of the present work was to assess the role of SUR1-subtype KATPchannels in antinocicpetion and hyperlocomotion of synthetic and semi-synthetic opioids.

Methods

Adult male and female mice wild-type (WT) and SUR1 deficient (KO) mice were assessed for mechanical and thermal antinociception after administration of either buprenorphine, fentanyl, or DAMGO. Potassium flux was assessed in the dorsal root ganglia and superficial dorsal horn cells in WT and KO mice. Hyperlocomotion was also assessed in WT and KO animals after buprenorphine, fentanyl, or DAMGO administration.

Results

SUR1 KO mice had attenuated mechanical antinociception after systemic administration of buprenorphine, fentanyl, and DAMGO. Potassium flux was also attenuated in the dorsal root ganglia and spinal cord cells after acute administration of buprenorphine and fentanyl. Hyperlocomotion after administration of morphine and buprenorphine was potentiated in SUR1 KO mice, but was not seen after administration of fentanyl or DAMGO.

Conclusions

These results suggest SUR1-subtype KATPchannels mediate the antinociceptive response of several classes of opioids (alkaloid and synthetic/semi-synthetic), but may not contribute to the “drug-seeking” behaviors of all classes of opioids.
Learning differentially shapes prefrontal and hippocampal activity during classical conditioning
Authors: Klee Jan L. , Souza Bryan C. , Battaglia Francesco P.
Published: December 2020

The ability to use sensory cues to inform goal directed actions is a critical component of intelligent behavior. To study how sound cues are translated into anticipatory licking during classical appetitive conditioning, we employed high-density electrophysiological recordings from the hippocampal CA1 area and the prefrontal cortex (PFC). CA1 and PFC neurons undergo distinct learning dependent changes at the single cell level and maintain representations of cue identity during anticipatory behavior at the population level. In addition, reactivation of task-related neuronal assemblies during hippocampal awake Sharp-Wave Ripples (aSWR) changed within individual sessions in CA1 and over the course of multiple sessions in PFC. Despite both areas being highly engaged and synchronized during the task, we found no evidence for coordinated single cell or assembly activity during conditioning trials or aSWR.
Summary Visualisations of Gene Ontology Terms with GO-Figure!
Authors: Reijnders Maarten JMF , Waterhouse Robert M
Published: December 2020

The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large- scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualisations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualisation tools and resources there is a lack of standalone open-source software solutions that facilitate systematic comparisons of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together GO terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar GO terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualisations of lists of GO terms, designed to support exploratory data analyses and multiple dataset comparisons.
Local and distributed cortical markers of effort expenditure during sustained goal pursuit
Authors: Patrick Lauren M. , Anderson Kevin M. , Holmes Avram J.
Published: December 2020

The adaptive adjustment of behavior in pursuit of desired goals is critical for survival. To accomplish this complex feat, individuals must weigh the potential benefits of a given course of action against time, energy, and resource costs. Prior research in this domain has greatly advanced understanding of the cortico-striatal circuits that support the anticipation and receipt of desired outcomes, characterizing core aspects of subjective valuation at discrete points in time. However, motivated goal pursuit is not a static or cost neutral process and the brain mechanisms that underlie individual differences in the dynamic updating of effort expenditure across time remain unclear. Here, 38 healthy right-handed participants underwent functional MRI (fMRI) while completing a novel paradigm to examine their willingness to exert physical effort over a prolonged trial, either to obtain monetary rewards or avoid punishments. During sustained goal pursuit, medial prefrontal cortex (mPFC) response scaled with trial-to-trial differences in effort expenditure as a function of both monetary condition and eventual task earnings. Multivariate pattern analysis (MVPA) searchlights were used to examine relations linking prior trial-level effort expenditure to subsequent brain responses to feedback. At reward feedback, whole-brain searchlights identified signals reflecting past effort expenditure in dorsal and ventral mPFC, encompassing broad swaths of frontoparietal and dorsal attention networks. These results suggest a core role for mPFC in scaling effort expenditure during sustained goal pursuit, with the subsequent tracking of effort costs following successful goal attainment extending to incorporate distributed brain networks that support executive functioning and externally oriented attention.

Significance Statement

Historically, much of the research on subjective valuation has focused on discrete points in time. Here, we examine brain responses associated with willingness to exert physical effort during the sustained pursuit of desired goals. Our analyses reveal a distributed pattern of brain activity encompassing aspects of ventral mPFC that tracks with trial-level variability in effort expenditure. Indicating that the brain represents echoes of effort at the point of feedback, searchlight analyses revealed signals associated with past effort expenditure in broad swaths of dorsal and medial PFC. These data have important implications for the study of how the brain’s valuation mechanisms contend with the complexity of real-world dynamic environments with relevance for the study of behavior across health and disease.
Characterising pre-clinical sub-phenotypic models of Acute Respiratory Distress Syndrome: an experimental ovine study
Authors: Millar Jonathan E , Wildi Karin , Bartnikowski Nicole , Bouquet Mahe , Hyslop Kieran , Passmore Margaret R , Ki Katrina K , See Hoe Louise E , Obonyo Nchafatso G , Neyton Lucile , Pedersen Sanne , Rozencwajg Sacha , Baillie J Kenneth , Bassi Gianluigi Li , Suen Jacky Y , McAuley Daniel F , Fraser John F
Published: December 2020

The Acute Respiratory Distress Syndrome (ARDS) describes a heterogenous population of patients with acute severe respiratory failure. However, contemporary advances have begun to identify distinct sub-phenotypes that exist within its broader envelope. These sub-phenotypes have varied outcomes and respond differently to several previously studied interventions. A more precise understanding of their pathobiology and an ability to prospectively identify them, may allow for the development of precision therapies in ARDS. Historically, animal models have played a key role in translational research, although few studies have so far assessed either the ability of animal models to replicate these sub-phenotypes or investigated the presence of sub-phenotypes within animal models. Here, in three ovine models of ARDS, using combinations of oleic acid and intravenous, or intratracheal lipopolysaccharide, we demonstrate the presence of sub-phenotypes which qualitatively resemble those found in clinical cohorts. Principal Components Analysis and partitional clustering reveal two clusters, differentiated by markers of shock, inflammation, and lung injury. This study provides the first preliminary evidence of ARDS phenotypes in pre-clinical models and develops a methodology for investigating this phenomenon in future studies.
DNA transduction inSodalisspecies: implications for the genetic modification of uncultured endosymbionts of insects
Authors: Keller Chelsea M. , Kendra Christopher G. , Bruna Roberto E. , Craft David , Pontes Mauricio H.
Published: December 2020

Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation ofEscherichia coliand a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing and promoting transduction in members of the bacterial genusSodalis, including the maternally inherited insect endosymbiontSodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.

A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherit nature of these associations, insect endosymbionts cannot be usually isolated in pure culture nor genetically manipulated. Here we use a broad-host range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad host range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.
The nucleotide messenger (p)ppGpp is a co-repressor of the purine synthesis transcription regulator PurR in Firmicutes
Authors: Anderson Brent W. , Schumacher Maria A. , Yang Jin , Turdiev Asan , Turdiev Husan , He Qixiang , Lee Vincent T. , Brennan Richard G. , Wang Jue D.
Published: December 2020

The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Yet despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria. Here we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes from soil bacteria to pathogens: (p)ppGpp serves as a co-repressor of the transcription factor PurR to downregulate purine biosynthesis. We identified PurR as a receptor of (p)ppGpp inBacillus anthracisand revealed that (p)ppGpp strongly enhances PurR binding to its regulon in theBacillus subtilisgenome. A co-structure reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of PRT enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractorypurRmutant fails to downregulate purine synthesis genes upon starvation. Our work establishes precedent of (p)ppGpp as a classical transcription co-repressor and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from the human intestinal tract to host-pathogen interfaces.
Efficacy of Biofilm Disrupters AgainstCandida aurisand OtherCandidaspecies
Authors: Cox Claudia A , Vazquez Jose A , Wakade Sushama , Bogacz Marek , Myntti Matthew , Manavathu Elias K
Published: December 2020

Background

C. aurishas become a globally emerging fungal pathogen, frequently reported to be multi-drug resistant, commonly found withStaphylococcus aureusin polymicrobial nosocomial infections. Although chlorhexidine (CHD) has been shown to be effective, it is associated with serious anaphylaxis reactions. Biofilm disrupters (BDs) are novel agents with a broad spectrum of antimicrobial activity. BDs have been used in the management of chronic wounds and to sterilize environmental surfaces. The goal of this study was to evaluate BDs against polymicrobial biofilms compared to CHD.

Methodology

We evaluated various BDs (BlastX, Torrent, NSSD) and CHD againstCandida sppandS. aureuspolymicrobial biofilms by zone of inhibition, biofilm, and time-kill assays. Effectiveness was based on the inhibition zone and the reduction of CFU, respectively, compared to the drug-free control.

Results

All BDs and CHD inhibitedC. aurisgrowth effectively in a concentration-dependent manner. Additionally, CHD and the BDs all showed excellent antimicrobial activity against polymicrobial biofilms. BDs were all highly effective against bothC. aurisisolates, whereas CHD was only moderately effective againstC. auris0386, suggesting resistance/tolerance. A comparative analysis of the BDs and CHD againstC. auris and C. albicansby biofilm kill-curves showed at least 99.999% killing.

Conclusions

All three BDs and CHD have excellent activity against differentCandidaspecies, includingC. auris. However, certain isolates ofC. aurisshowed resistance/tolerance to CHD, but not to the BDs. The fungicidal activity of these novel agents will be valuable in eradicating surface colonization ofCandida spp, includingC. auris.
Potentiating CD8+T cell antitumor activity by targeting the PCSK9/LDLR axis
Authors: Yuan Juanjuan , Cai Ting , Zheng Xiaojun , Ren Yangzi , Qi Jinwen , Lu Xiaofei , Chen Huihui , Lin Huizhen , Chen Zijie , Liu Mengnan , He Shangwen , Chen Qijun , Feng Siyang , Wu Yinjun , Zhang Zhenhai , Ding Yanqing , Yang Wei
Published: December 2020

Metabolic regulation has proven to play a critical role in T cell antitumor immunity. Cholesterol metabolism is a key component of this response but remains largely unexplored. Herein, we found that the LDL receptor (LDLR), which has been previously identified as a transporter for cholesterol and fatty acids, plays a pivotal role in regulating CD8+T cell antitumor activity, with the genetic ablation of LDLR significantly attenuating CD8+T cell activation and clonal expansion. Additionally, we found that LDLR interacts with the T-cell receptor (TCR) signalosome and regulates TCR signaling, facilitating CD8+T cell activation and effector function. Furthermore, we found that the tumor microenvironment downregulates CD8+T cell LDLR levels and TCR signaling via tumor cell-derived PCSK9, which binds and prevents the recycling of LDLR and TCR into the plasma membrane. Our findings indicate that genetic deletion or pharmacological inhibition of PCSK9 in tumor cells can enhance the antitumor activity of CD8+T cells by alleviating the tumor microenvironment’s suppressive effect on CD8+T cells and consequently inhibit tumor progression. While previously established as a hyperlipidemia target, this study highlights PCSK9 as a potential target for cancer immunotherapy as well.
Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice
Authors: Schukken Klaske M. , Zhu Yinan , Bakker Petra L. , Harkema Liesbeth , Youssef Sameh A. , de Bruin Alain , Foijer Floris
Published: December 2020

Chromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last two decades. These studies have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of intestinal epithelia, substantial weight loss, and death within 10 days after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the low proliferation rate in these tissues. We conclude that high-grade CINin vivoin adult mice is most toxic to intestinal epithelia, presumably due to the high cell turnover in this tissue.
Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome
Authors: Fodelianakis Stilianos , Washburne Alex D. , Bourquin Massimo , Pramateftaki Paraskevi , Kohler Tyler J. , Styllas Michail , Tolosano Matteo , De Staercke Vincent , Schön Martina , Busi Susheel Bhanu , Brandani Jade , Wilmes Paul , Peter Hannes , Battin Tom J.
Published: December 2020

Microdiversity, the organization of microorganisms into groups with closely related but ecologically different sub-types, is widespread and represents an important linchpin between microbial ecology and evolution. However, the drivers of microdiversification remain largely unknown. Here we show that selection promotes microdiversity in the microbiome associated with sediments in glacier-fed streams (GFS). Applying a novel phylogenetic framework, we identify several clades that are under homogeneous selection and that contain genera with higher levels of microdiversity than the rest of the genera. Overall these clades constituted ∼44% and ∼64% of community α-diversity and abundance, and both percentages increased further in GFS that were largely devoid of primary producers. Our findings show that strong homogeneous selection drives the microdiversification of specialized microbial groups putatively underlying their success in the extreme environment of GFS. This microdiversity could be threatened as glaciers shrink, with unknown consequences for microbial diversity and functionality in these ecosystems.
High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion
Authors: Zhong Haining , Massengill Crystian I. , Muniak Michael A. , Ma Lei , Qin Maozhen , Petrie Stefanie Kaech , Mao Tianyi
Published: December 2020

Precise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method calledCRISPR-mediated insertion ofexon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing. CRISPIE inserts a designer donor module, which consists of an exon encoding the protein sequence flanked by intron sequences, into an intronic location in the target gene. INDELs at the insertion junction will be spliced out, leaving mRNAs nearly error-free. We used CRISPIE to fluorescently label endogenous proteins in neuronsin vivowith previously unachieved efficiency. We demonstrate that this method is broadly applicable, and that the insert can be readily removed later. CRISPIE permits protein sequence insertion with high fidelity, efficiency, and flexibility.
Transformation of European ash (Fraxinus excelsiorL.) callus as a starting point for understanding the molecular basis of ash dieback
Authors: Hebda Anna , Liszka Aleksandra , Zgłobicki Piotr , Nawrot-Chorabik Katarzyna , Lyczakowski Jan J.
Published: December 2020

Plant genetic engineering requires transfer of genetic material into plant cells, a process that is frequently challenging for tree species. Here we report first successful genetic transformation of European ash (Fraxinus excelsior). The protocol relies on the use ofAgrobacterium tumefaciensto transform callus tissue derived from embryos ofF. excelsior. In our experiments, we use the β-glucuronidase (GUS) reporter system to demonstrate transformation of ash callus tissue. Moreover, we describe an antibiotic-resistance based selection process enabling formation of stable transgenic callus lines. Since ash dieback threatens the long-term stability of many nativeF. excelsiorpopulations, we hope that the transformation techniques described in this manuscript will facilitate rapid progress in uncovering the molecular basis of the disease and mechanisms used by trees to resist it.
Identification of low micromolar SARS-CoV-2 Mproinhibitors from hits identified byin silicoscreens
Authors: Rossetti Giacomo G. , Ossorio Marianna , Barriot Samia , Tropia Laurence , Dionellis Vasilis S. , Gorgulla Christoph , Arthanari Haribabu , Mohr Peter , Gamboni Remo , Halazonetis Thanos D.
Published: December 2020

Mpro, also known as 3CLpro, is the main protease of the SARS-CoV-2 coronavirus and, as such, is essential for the viral life cycle. Two studies have each screened and rankedin silicomore than one billion chemical compounds in an effort to identify putative inhibitors of Mpro. More than five hundred of the seven thousand top-ranking hits were synthesized by an external supplier and examined with respect to their activity in two biochemical assays: a protease activity assay and a thermal shift assay. Two clusters of chemical compounds with Mproinhibitory activity were identified. An additional five hundred molecules, analogues of the compounds in the two clusters described above, were also synthesized and characterizedin vitro. The study of the analogues revealed that the compounds of the first cluster acted by denaturing Mproand might denature other proteins as well. In contrast, the compounds of the second cluster targeted Mprowith much greater specificity and enhanced its melting temperature, consistent with the formation of stable Mpro-inhibitor complexes. The most active compounds of the second cluster exhibited IC50values between 4 and 7 μM and their chemical structure suggests that they could serve as leads for the development of potent Mproinhibitors.
Molecular basis of the logical evolution of the novel coronavirus SARS-CoV-2: A comparative analysis
Authors: Dwivedy Abhisek , Murmu Krushna Chandra , Ahmad Mohammed , Prasad Punit , Biswal Bichitra Kumar , Aich Palok
Published: December 2020

A novel disease, COVID-19, is sweeping the world since end of 2019. While in many countries, the first wave is over, but the pandemic is going through its next phase with a significantly higher infectability. COVID-19 is caused by the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that seems to be more infectious than any other previous human coronaviruses. To understand any unique traits of the virus that facilitate its entry into the host, we compared the published structures of the viral spike protein of SARS-CoV-2 with other known coronaviruses to determine the possible evolutionary pathway leading to the higher infectivity. The current report presents unique information regarding the amino acid residues that were a) conserved to maintain the binding with ACE2 (Angiotensin-converting enzyme 2), and b) substituted to confer an enhanced binding affinity and conformational flexibility to the SARS-CoV-2 spike protein. The present study provides novel insights into the evolutionary nature and molecular basis of higher infectability and perhaps the virulence of SARS-CoV-2.
An acute dose of intranasal oxytocin rapidly increases maternal communication and maintains maternal care in primiparous postpartum California mice
Authors: Guoynes Caleigh D. , Marler Catherine A.
Published: December 2020

Maternal-offspring communication and care are essential for offspring survival. Oxytocin (OXT) is known for its role in initiation of maternal care, but whether OXT can rapidly influence maternal behavior or ultrasonic vocalizations (USVs; above 50 kHz) has not been examined. To test for rapid effects of OXT, California mouse mothers were administered an acute intranasal (IN) dose of OXT (0.8 IU/kg) followed by a separation test with three phases: habituation with pups in a new testing chamber, separation via a wire mesh, and finally reunion with pups. We measured maternal care, maternal USVs, and pup USVs. In mothers, we primarily observed simple sweep USVs, a short downward sweeping call around 50 kHz, and in pups we only observed pup whines, a long call with multiple harmonics ranging from 20 kHz to 50 kHz. We found that IN OXT rapidly and selectively enhanced the normal increase in maternal simple sweep USVs when mothers had physical access to pups (habituation and reunion), but not when mothers were physically separated from pups. Maternal-pup USVs were correlated upon reunion, but IN OXT did not influence this correlation. Finally, mothers given IN OXT showed a more positive change in retrievals/carrying and greater total maternal care upon reunion. Behavioral changes were specific to maternal behaviors (e.g. retrievals) as mothers given IN OXT did not differ from controls in stress-related behaviors (e.g. freezing). Overall, these findings highlight the rapid effects and context-dependent effect a single dose of IN OXT has on both maternal USV production and offspring care.
Confocal imaging capacity on a widefield microscope using a spatial light modulator
Authors: Wang Yao L. , Grooms Noa W. F. , Civale Sabrina C. , Chung Samuel H.
Published: December 2020

Confocal microscopes can reject out-of-focus and scattered light; however, widefield microscopes are far more common in biological laboratories due to their accessibility and lower cost. We report confocal imaging capacity on a widefield microscope by adding a spatial light modulator (SLM) and utilizing custom illumination and acquisition methods. We discuss our illumination strategy and compare several procedures for postprocessing the acquired image data. We assessed the performance of this system for rejecting out-of-focus light by comparing images taken using our widefield microscope, our SLM-enhanced setup, and a commercial confocal microscope. The optical sectioning capability, assessed on thin fluorescent film, was 0.85 ± 0.04 μm for our SLM-enhanced setup and 0.68 ± 0.04 μm for a confocal microscope, while a widefield microscope exhibited no sectioning capability. We demonstrate our setup by imaging the same set of neurons inC. eleganson widefield, SLM, and confocal microscopes. SLM enhancement greatly reduces background from the cell body, allowing visualization of dim fibers nearby. Our SLM-enhanced setup identified 93% of the dim neuronal fibers seen in confocal images while a widefield microscope only identified 48% of the same fibers. Our microscope add-on represents a very simple (2-component) and inexpensive (<$600) approach to enable widefield microscopes to optically section thick samples.
Identification of a High-frequency Intra-host SARS-CoV-2 spike Variant with Enhanced Cytopathic and Fusogenic Effect
Authors: Rocheleau Lynda , Laroche Geneviève , Fu Kathy , Stewart Corina M , Mohamud Abdulhamid O , Côté Marceline , Giguère Patrick M , Langlois Marc-André , Pelchat Martin
Published: December 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that is continuously evolving. Although its RNA-dependent RNA polymerase exhibits some exonuclease proofreading activity, viral sequence diversity can be produced by replication errors and host factors. A diversity of genetic variants can be observed in the intra-host viral population structure of infected individuals. Most mutations will follow a neutral molecular evolution and won’t make significant contributions to variations within and between infected hosts. Herein, we profiled the intra-sample genetic diversity of SARS-CoV-2 variants using high-throughput sequencing datasets from 15,289 infected individuals and infected cell lines. Most of the genetic variations observed, including C->U and G->U, were consistent with errors due to heat-induced DNA damage during sample processing and/or sequencing protocols. Despite high mutational background, we identified recurrent intra-variable positions in the samples analyzed, including several positions at the end of the gene encoding the viral Spike (S) protein. Strikingly, we observed a high-frequency C->A missense mutations resulting in the S protein lacking the last 20 amino acids (SΔ20). We found that this truncated S protein undergoes increased processing and increased syncytia formation, presumably due to escaping M protein retention in intracellular compartments. Our findings suggest the emergence of a high-frequency viral sublineage that is not horizontally transmitted but potentially involved in intra-host disease cytopathic effects.

IMPORTANCE

The mutation rate and evolution of RNA viruses correlate with viral adaptation. While most mutations do not have significant contributions to viral molecular evolution, some are naturally selected and cause a genetic drift through positive selection. Many recent SARS-CoV-2 variants have been recently described and show phenotypic selection towards more infectious viruses. Our study describes another type of variant that does not contribute to inter-host heterogeneity but rather phenotypic selection toward variants that might have increased cytopathic effects. We identified that a C-terminal truncation of the Spike protein removes an important ER-retention signal, which consequently results in a Spike variant that easily travels through the Golgi toward the plasma membrane in a pre-activated conformation, leading to increased syncytia formation.
CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells
Authors: Kim Kyoung-Dong , Cho Subin , Kim Taelyn , Huh Sora , Kim Lina , Tanizawa Hideki , Shin Jae-Ho , Kanda Teru , Won Kyoung Jae , Lieberman Paul M. , Cho Hyosun , Kang Hyojeung
Published: December 2020

EBV latent infection in gastric carcinoma (GC) cells is characterized by distinct viral gene expression programs. CCCTC-binding factor (CTCF) is a chromatin structural factor that has been involved in coordinated chromatin interactions between multiple loci of Epstein-Barr virus (EBV) genes. Here, we investigate the role of CTCF in regulating EBV gene expression and chromosome conformation in model of EBV-associated gastric carcinoma (EBVaGC). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) against CTCF revealed 16 CTCF binding sites (BS) in EBV genome of EBVaGC, SNU719 cells. Among the CTCF BSs, one site named as BARTp (BamHI A right transcript promoter) CTCF BS is located at upstream of 11.8-kb BART region (EBV genome: 139724-151554) and was not yet defined its biological functions in EBV life cycle. EBV BART encodes a complex miRNA cluster of highly spliced transcripts that is implicated in EBV cancer pathogenesis. This present study investigated the functional role of the CTCF binding site at BARTp (BARTp CTCF BS) in regulating EBV gene transcription and EBV three-dimensional (3D) genome structure as DNA loop maker. Circular chromatin confirmation capture (4C)-seq and chromatin confirmation capture (3C)-semi-quantitative(sq)PCR assays using SNU719 cells revealed that BARTp CTCF BS interacts with CTCF BSs of LMP1/2, Cp/OriP, and Qp in EBV genome. We generated mutations in BARTp CTCF BS (S13) in bacmids with (BART+) or without (BART−) the 11.8-kb BART transcript unit (B(+/−)). ChIP-qPCR assay demonstrated that CTCF binding was ablated from BARTp in EBV B(+/−) S13−genomes (mutant S13), elevated at several other sites such asLMP1, OriP, andCpin EBV B(-) (BART−) S13−genome, and decreased at the same sites in EBV B(+) S13−genome. Infection assay showed that BARTp CTCF BS mutation reduced infectivity, while BART transcript deletion has no detectable effects. Gene expression tests showed thatEBNA1was highly downregulated in B(+/−) S13−EBVs related to B(+/−) S13+EBVs (wild-type S13).LMP1andBZLF1were more downregulated in B(-) S13−EBV than B(+) S13−EBV. Taken together, these findings suggest that the CTCF binding and BART region contribute to EBV 3D genome structure via a cluster of DNA loops formed by BARTp CTCF BS (S13) and are important for coordinated viral gene expression and EBV infectivity.