bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epitranscriptomic Dysregulation in Stress-induced Psychopathologies
Authors: Ohtan Wang Dan , Joshi Kandarp , Gururajan Anand 
Published: February 2021

AbstractTo date, over 100 different chemical modifications to RNA have been identified. Collectively known as the epitranscriptome, these modifications function to regulate RNA stability and as such, represent another mechanistic layer of post-transcriptional gene regulation. N6-methyladenosine (m6A) is the most common RNA modification in the mammalian brain and has been implicated in a number of processes relevant to neurodevelopment, brain function and behaviour. Here, following brief descriptions on epitranscriptomic mechanisms, we will review the literature on the potential functions of the m6A-methylome in fine-tuning gene expression which include prescribing localisation of transcripts in distal compartments as well as interactions with microRNAs and long non-coding RNAs. We will then discuss findings from rodent and human studies for stress-induced disorders - major depression and post-traumatic stress disorder – which support a hypothesis for a dysregulation of the m6A-methylome and the m6A-machinery in the pathophysiology. To support this, we have included a bioinformatic analysis of publicly available single-cell RNA-sequencing and bulk transcriptomics datasets which suggests an altered m6A-methylome as a consequence of dysregulated cell- and regionally-specific expression of key enzymes involved in the ‘writing, reading and erasing’ of m6A. We hope this review will generate further interest in the field of epitranscriptomics, opening up new lines of research into its involvement in psychiatric disorders.
Cell-type specific arousal-dependent modulation of thalamic activity in the lateral geniculate nucleus
Authors: Molnár Benedek , Sere Péter , Bordé Sándor , Koós Krisztián , Horváth Péter , Lőrincz Magor L. 
Published: February 2021

ABSTRACTState dependent thalamocortical activity is important for sensory coding, oscillations and cognition. The lateral geniculate nucleus (LGN) relays visual information to the cortex, but the state dependent spontaneous and visually evoked activity of LGN neurons in awake behaving animals remains controversial. Using a combination of pupillometry, extracellular and intracellular recordings from identified LGN neurons we show that thalamocortical neurons and interneurons are distinctly correlated to arousal forming two complementary coalitions. Intracellular recordings indicated that the membrane potential of LGN TC neurons was tightly correlated to fluctuations in pupil size. Inactivating the corticothalamic feedback to the LGN suppressed the arousal dependency of LGN neurons. Taken together our results show that LGN neuronal membrane potential and action potential output are dynamically linked to arousal dependent brain states in awake mice and this might have important functional implications.
Fetal gut colonization: meconium does not have a detectable microbiota before birth
Authors: Kennedy Katherine M. , Gerlach Max J. , Adam Thomas , Heimesaat Markus M. , Rossi Laura , Surette Michael G. , Sloboda Deborah M. , Braun Thorsten 
Published: February 2021

AbstractMicrobial colonization of the human intestine impacts host metabolism and immunity, however when colonization occurs is unclear. Although numerous studies have reported bacterial DNA in first-pass meconium samples, these samples are collected hours to days after birth. We investigated whether bacteria could be detected in meconium prior to birth. Fetal meconium (n = 20) was collected by rectal swab during elective breech Cesarean sections without labour prior to antibiotics and compared to technical and procedural controls (n = 5), first-pass meconium (neonatal meconium; n = 14), and infant stool (n = 25). Unlike first-pass meconium, no microbial signal distinct from negative controls was detected in fetal meconium by 16S rRNA gene sequencing. Additionally, positive aerobic (n = 10 of 20) and anaerobic (n = 12 of 20) clinical cultures of fetal meconium (13 of 20 samples positive in at least one culture) were identified as likely skin contaminants, most frequently Staphylococcus epidermidis, and not detected by sequencing in most samples (same genera detected by culture and sequencing in 2 of 13 samples with positive culture). We conclude that fetal gut colonization does not occur before birth, and that microbial profiles of neonatal meconium reflect populations acquired during and after birth.
A glimpse into the diverse cellular immunity against SARS-CoV-2
Authors: Chang Cheng-Wei , Liu Yuchen , Jiao Cheng , Liu Hongwei , Chen Xiaochuan , Chang Lung-Ji 
Published: February 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific cellular immune response may prove to be essential for long-term immune protection against the novel coronavirus disease 2019 (COVID-19). To assess COVID-19-specific immunity in the population, we synthesized selected peptide pools of SARS-CoV-2 structural and functional proteins, including Spike (S), Membrane (M), Envelope (E), Nucleocapsid (N) and Protease (P) as target antigens. Survey of the T cell precursur frequencies in healthy individuals specific to these viral antigens demonstrated a diverse cellular immunity, including high, medium, low and no responders. This was further confirmed by in vitro induction of anti-SARS-CoV-2 T cell immune responses using dendritic cell (DC)/T cell coculture, which supported the corresponding T cell precursor frequencies in each of the individuals tested. In general, the combination of all five viral antigen pools induced the strongest cellular immune response, yet individual donors responded differently to different viral antigens. Importantly, in vitro restimulation of the T cells with the DC-peptides induced increased anti-viral immune responses in all individuals even in the no responders, suggesting that repeated antigen stimulation could elicit a broad protection in immune naïve population. Our analysis recapitulates the critical role of cellular immunity in fighting COVID-19 and the importance of analyzing anti-SARS-CoV-2 T cell response in addition to antibody response in the population.ImportanceFacing the rapid evolving SARS-CoV-2 variants in the world, current emphasis on antibody-producing vaccines needs a quick revisit. The virus-specific cellular immunity may prove to be essential for long-term protection against COVID-19. This study designed a series of antigenic peptides encompassing the conserved and/or essential domains of Spike (S), Membrane (M), envelope (E), Nucleocapsid (N) and Protease (P) as targets to assess Covid-19-specific immunity in the population. The results demonstrated a diverse cellular immunity, including high, medium, low and no responders. This was verified by in vitro generation of anti-SARS-CoV-2 T-cells from these subjects. The study suggested that individuals responded differently to the different viral antigens, and importantly, repeated stimulation could produce virus specific T cells in all individuals, including the no responders. This study illustrates the needs for assessing anti-viral cellular immunity in addition to antibody response in the general population.
CK2 phosphorylation of human papillomavirus 16 E2 on serine 23 promotes interaction with TopBP1 and is critical for E2 plasmid retention function
Authors: Prabhakar Apurva T. , James Claire D. , Das Dipon , Otoa Raymonde , Day Matthew , Burgner John , Fontan Christian T. , Wang Xu , Wieland Andreas , Donaldson Mary M. , Bristol Molly L. , Li Renfeng , Oliver Anthony W. , Pearl Laurence H. , Smith Brian O. , Morgan Iain M. 
Published: February 2021

AbstractDuring the human papillomavirus 16 (HPV16) life cycle, the E2 protein interacts with host factors to regulate viral transcription, replication and genome segregation/retention. Our understanding of host partner proteins and their roles in E2 functions remains incomplete. Here, we demonstrate that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1in vitroandin vivo, and that E2 is phosphorylated on this residue during the HPV16 life cycle. We investigated the consequences of mutating serine 23 on E2 functions. E2-S23A activates and represses transcription identically to E2-WT (wild-type), and E2-S23A is as efficient as E2-WT in transient replication assays. However, E2-S23A has compromised interaction with mitotic chromatin when compared with E2-WT. In E2-WT cells, both E2 and TopBP1 levels increase during mitosis when compared with vector control cells. In E2-S23A cells, neither E2 nor TopBP1 levels increase during mitosis. We next tested whether this difference in E2-S23A levels during mitosis disrupts E2 plasmid retention function. We developed a novel plasmid retention assay and demonstrate that E2-S23A is deficient in plasmid retention when compared with E2-WT. siRNA targeted knockdown of TopBP1 abrogates E2-WT plasmid retention function. Introduction of the S23A mutation into the HPV16 genome resulted in delayed immortalization of human foreskin keratinocytes (HFK) and higher episomal viral genome copy number in resulting established HFK. Overall, our results demonstrate that CK2 phosphorylation of E2 on serine 23 promotes interaction with TopBP1, which is critical for E2 plasmid retention function and in HPV16 immortalization of keratinocytes.ImportanceHuman papillomaviruses are causative agents in around 5% of all cancers, with no specific anti-viral therapeutics available for treating infections or resultant cancers. In this report, we demonstrate that phosphorylation of HPV16 E2 by CK2 promotes formation of a complex formation with the cellular protein TopBP1in vitroandin vivo. This complex results in stabilization of E2 during mitosis and mediates plasmid retention by E2. This function promotes the partitioning of viral genomes into the nuclei of daughter cells following mitosis. We demonstrate that CK2 phosphorylates E2 on serine 23in vivo, and that CK2 inhibitors disrupt the E2-TopBP1 complex. Mutation of E2 serine 23 to alanine disrupts the HPV16 life cycle, demonstrating a critical function for this residue. Together, our results suggest that CK2 inhibitors may disrupt the E2-TopBP1 dependent HPV16 life cycle and potentially kill HPV16 positive cancers, which lays a molecular foundation to develop novel therapeutic approaches for combating HPV16 disease.
Cost-effectiveness of polygenic risk profiling for primary open-angle glaucoma in the United Kingdom and Australia
Authors: Liu Qinqin , Davis John , Han Xikun , Mackey David A , MacGregor Stuart , Craig Jamie E , Si Lei , Hewitt Alex W 
Published: February 2021

ABSTRACTObjectivePrimary open-angle glaucoma (POAG) is the most common subtype of glaucoma worldwide. Early diagnosis and intervention is proven to slow disease progression and reduce disease burden. Currently, population-based screening for POAG is not generally recommended due to cost. In this study, we evaluate the cost-effectiveness of polygenic risk profiling as a screening tool for POAG.Methods and AnalysisWe used a Markov cohort model to evaluate the cost-effectiveness of implementing polygenic risk profiling as a new POAG-screening approach in the UK and Australia. Six health states were included in this model: death, early, mild, moderate, severe, and healthy individuals. The evaluation was conducted from the healthcare payer’s perspective. We used the best available published data to calculate prevalence, transition probabilities, utility and other parameters for each health state and age group. The study followed the CHEERS checklist. Our main outcome measure was the incremental cost-effectiveness ratio (ICER) and secondary outcomes were years of blindness avoided per person and a ‘Blindness ICER’. We did one-way and two-way deterministic and probabilistic sensitivity analyses to reflect the uncertainty around predicting ICERs.ResultsOur proposed genetic screening programme for POAG in Australia is predicted to result in ICER of AU$34,252 (95% CI AU$21,324-95,497) and would avoid 1 year of blindness at ICER of AU$13,359 (95% CI: AU$8,143-37,448). In the UK, this screening is predicted to result in ICER of £24,783 (13,373-66,960) and would avoid 1 year of blindness at ICER of £10,095 (95%CI: £5,513-27,656). Findings were robust in all sensitivity analyses. Using the willingness to pay thresholds of $54,808 and £30,000, the proposed screening model is 79.2% likely to be cost-effective in Australia and is 60.2% likely to be cost-effective in the UK, respectively.ConclusionsWe describe and model the cost-efficacy of incorporating a polygenic risk score for POAG screening in Australia and the UK. Although the level of willingness to pay for Australian Government is uncertain, and the ICER range for the UK is broad, we showed a clear target strategy for early detection and prevention of advanced POAG in these developed countries.Copyrightthe Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd to permit this article (if accepted) to be published in BMJ editions and any other BMJPGL products and sublicences such use and exploit all subsidiary rights, as set out in our licence.
A NOVEL AIR-DRIED MULTIPLEX HIGH RESOLUTION MELT ASSAY FOR THE DETECTION OF EXTENDED SPECTRUM BETA-LACTAMASE AND CARBAPENEMASE GENES
Authors: Cubas-Atienzar Ana I. , Williams Christopher T. , Karkey Abhilasha , Dongol Sabina , Sulochana Manandhar , Rajendra Shrestha , Hobbs Glyn , Evans Katie , Musicha Patrick , Feasey Nicholas , Cuevas Luis E. , Adams Emily R. , Edwards Thomas 
Published: February 2021

ABSTRACTHere we describe the development and evaluation of a novel an air-dried high-resolution melt (HRM) assay to detect eight major extended spectrum beta-Lactamase (ESBL) (SHV and CTXM groups 1 and 9) and Carbapenemase (NDM, IMP, KPC, VIM and OXA-48) genes that cause antimicrobial resistance. The assay was evaluated using 440 DNA samples extracted from bacterial isolates from Nepal, Malawi and UK and 390 clinical Enterobacteriaceae isolates with known resistance phenotypes from Nepal. The sensitivity and specificity for detecting the ESBL and Carbapenemase genes in comparison to the reference gel-base PCR and sequencing was 94.7% (95%CI: 92.5%-96.5%) and 99.2% (95%CI: 98.8%-99.5%) and 98.5% (95%CI: 97.0%-99.4%) and 98.5% (95%CI: 98.0%-98.9%) when compared to the original wet format. The overall phenotypic agreement was 91.1% (95%CI: 90.0%-92.9%) on predicting resistance to cefotaxime and carbapenems. We observed good inter-machine reproducibility of the air-dried HRM assay using the Rotor-Gene Q, QuantStudio™ 5, CFX96, LightCycler® 480 and MIC. Assay stability upon storage in the fridge (6.2°C ± 0.9), room temperature (20.35°C ± 0.7) and oven (29.7°C ± 1.4) were assessed at six time points for eight months and no loss of sensitivity occurred under all conditions. We present here a ready-to-use air-dried HRM-PCR assay that offers an easy, thermostable, fast and accurate tool for the detection of ESBL and Carbapenamase genes to improve AMR diagnosis and treatment.
Mobility and COVID-19 in Andorra: Country-scale analysis of high-resolution mobility patterns and infection spread
Authors: Doorley Ronan , Berke Alex , Noyman Ariel , Alonso Luis , Ribó Josep , Arroyo Vanesa , Pons Marc , Larson Kent 
Published: February 2021

AbstractIn the absence of effective vaccines, non-pharmaceutical interventions, such as mobility restrictions, were globally adopted as critically important strategies for curbing the spread of COVID-19. However, such interventions come with immense social and economic costs and the relative effectiveness of different mobility restrictions are not well understood. This study analyzed uniquely comprehensive datasets for the entirety of a small country, consisting of serology data, telecoms data, and COVID-19 case reports, in order to examine the relationship between mobility and transmission of COVID-19.Andorra is a small European country where tourism is a large part of the economy. Stringent mobility restrictions were put in place in Spring 2020. Additionally, 91% of the population participated in a voluntary COVID-19 serology testing programme and those data were made available for this study. Furthermore, high resolution telecoms data for the entire population were available for analysis of mobility and proximity patterns. A set of mobility metrics were developed to indicate levels of crowding, stay-at-home rates, trip-making and contact with tourists. Mobility metrics were compared to infection rates across communities and transmission rate over time.Several of these metrics were highly correlated with transmission rate, with a lead time of approximately 18 days, with some metrics more highly correlated than others. There was a stronger correlation for measures of crowding and inter-community trip-making, and a weaker correlation for total trips (including intra-community trips) and stay-at-homes rates.
Conservation and Convergence of Genetic Architecture in the Adaptive Radiation ofAnolisLizards
Authors: McGlothlin Joel W. , Kobiela Megan E. , Wright Helen V. , Kolbe Jason J. , Losos Jonathan B. , Brodie Edmund D. 
Published: February 2021

ABSTRACTTheGmatrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However,Gcan evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution ofGin similar environments would suggest thatGevolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation ofAnolislizards to ask whether convergence ofGaccompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measuredGin seven species representing three ecomorphs (trunk-crown, trunk- ground, and grass-bush). We found that the overall structure ofGdoes not converge. Instead, the structure ofGis well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements ofGshowed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution ofG, even as its overall structure remains conserved.
Magnetically-Propelled Fecal Surrogates for Modeling the Impact of Solid-Induced Shear Forces on Primary Colonic Epithelial Cells
Authors: Hinman Samuel S. , Huling Jennifer , Wang Yuli , Wang Hao , Bretherton Ross C. , DeForest Cole A. , Allbritton Nancy L. 
Published: February 2021

ABSTRACTThe colonic epithelium is continuously exposed to an array of biological and mechanical stimuli as its luminal contents are guided over the epithelial surface through regulated smooth muscle contraction. In this report, the propulsion of solid fecal contents over the colonic epithelium is recapitulated through noninvasive actuation of magnetic agarose hydrogels over primary intestinal epithelial cultures, in contrast to the vast majority of platforms that apply shear forces through liquid microflow. Software-controlled magnetic stepper motors enable experimental control over the frequency and velocity of these events to matchin vivopropulsive contractions, while the integration of standardized well plate spacing facilitates rapid integration into existing assay pipelines. The application of these solid-induced shear forces did not deleteriously affect cell monolayer surface coverage, viability, or transepithelial electrical resistance unless the device parameters were raised to a 50× greater contraction frequency and 4× greater fecal velocity than those observed in healthy humans. At a frequency and velocity that is consistent with average human colonic motility, differentiation of the epithelial cells into absorptive and goblet cell phenotypes was not affected. Protein secretion was modulated with a two-fold increase in luminal mucin-2 secretion and a significant reduction in basal interleukin-8 secretion. F-actin, zonula occludens-1, and E-cadherin were each present in their proper basolateral locations, similar to those of static control cultures. While cellular height was unaffected by magnetic agarose propulsion, several alterations in lateral morphology were observed including decreased circularity and compactness, and an increase in major axis length, which align with surface epithelial cell morphologies observedin vivoand may represent early markers of luminal exfoliation. This platform will be of widespread utility for the investigation of fecal propulsive forces on intestinal physiology, shedding light on how the colonic epithelium responds to mechanical cues.HIGHLIGHTSMagnetic nanoparticle-embedded agarose hydrogels were developed as surrogates for human fecesSoftware-controlled magnetic motors enable programmable studies of colonic motilityPropulsive shear forces were optimized for primary cell viability, surface coverage, and electrical resistanceMucus production and cytokine secretion were modulated by magnetic agarose propulsionStructural and cytoskeletal proteins remain properly distributed with alterations in lateral cell morphology
Optogenetic silencing of neurotransmitter release with a naturally occurring invertebrate rhodopsin
Authors: Mahn Mathias , Saraf-Sinik Inbar , Patil Pritish , Pulin Mauro , Bitton Eyal , Karalis Nikolaos , Bruentgens Felicitas , Palgi Shaked , Gat Asaf , Dine Julien , Wietek Jonas , Davidi Ido , Levy Rivka , Litvin Anna , Zhou Fangmin , Sauter Kathrin , Soba Peter , Schmitz Dietmar , Lüthi Andreas , Rost Benjamin R. , Wiegert J. Simon , Yizhar Ofer 
Published: February 2021

AbstractInformation is carried between brain regions through neurotransmitter release from axonal presynaptic terminals. Understanding the functional roles of defined neuronal projection pathways in cognitive and behavioral processes requires temporally precise manipulation of their activityin vivo. However, existing optogenetic tools have low efficacy and off-target effects when applied to presynaptic terminals, while chemogenetic tools are difficult to control in space and time. Here, we show that a targeting-enhanced mosquito homologue of the vertebrate encephalopsin (eOPN3) can effectively suppress synaptic transmission through the Gi/osignaling pathway. Brief illumination of presynaptic terminals expressing eOPN3 triggers a lasting suppression of synaptic output that recovers spontaneously within minutesin vitroas well asin vivo. In freely moving mice, eOPN3-mediated suppression of dopaminergic nigrostriatal afferents leads to an ipsiversive rotational bias. We conclude that eOPN3 can be used to selectively suppress neurotransmitter release at synaptic terminals with high spatiotemporal precision, opening new avenues for functional interrogation of long-range neuronal circuitsin vivo.