bluuebunny/crossref_metadata_2025 huggingface dataset:
Altered calcium signaling in Bergmann glia contributes to Spinocerebellar ataxia type-1
Authors: Noriega-Prieto Jose Antonio , Nanclares Carmen , Labrada-Moncada Francisco E. , Cvetanovic Marija , Araque Alfonso , Kofuji Paulo
Published: May 2023

Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by an abnormal expansion of glutamine (Q) encoding CAG repeats in theATAXIN1(ATXN1) gene and characterized by progressive cerebellar ataxia, dysarthria, and eventual deterioration of bulbar functions. SCA1 shows severe degeneration of cerebellar Purkinje cells (PCs) and activation of Bergmann glia (BG), a type of cerebellar astroglia closely associated with PCs. Using electrophysiological recordings, confocal imaging and chemogenetic approaches, we have investigated the electrical intrinsic and synaptic properties of PCs and the physiological properties of BG in SCA1 mouse model expressing mutant ATXN1 only in PCs. PCs of SCA1 mice displayed lower spontaneous firing rate and larger medium and slow afterhyperpolarization currents (mIAHPand sIAHP) than wildtype mice, whereas the properties of the synaptic inputs were unaffected. BG of SCA1 mice showed higher calcium hyperactivity and gliotransmission, manifested higher frequency of NMDAR-mediated slow inward currents (SICs) in PC. Preventing the BG calcium hyperexcitability of SCA1 mice by loading BG with the calcium chelator BAPTA restored mIAHPand sIAHPand spontaneous firing rate of PCs to similar levels of wildtype mice. Moreover, mimicking the BG hyperactivity by activating BG expressing Gq- DREADDs in wildtype mice reproduced the SCA1 pathological phenotype of PCs, i.e., enhancement of mIAHPand sIAHPand decrease of spontaneous firing rate. These results indicate that the intrinsic electrical properties of PCs, but not their synaptic properties, were altered in SCA1 mice, and that these alterations were associated with the hyperexcitability of BG. Moreover, preventing BG hyperexcitability in SCA1 mice and promoting BG hyperexcitability in wildtype mice prevented and mimicked, respectively, the pathological electrophysiological phenotype of PCs. Therefore, BG plays a relevant role in the dysfunction of the electrical intrinsic properties of PCs in SCA1 mice, suggesting that they may serve as potential targets for therapeutic approaches to treat the spinocerebellar ataxia type 1.
A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions
Authors: Petkantchin Remy , Rousseau Alexandre , Eker Omer , Boudjeltia Karim Zouaoui , Raynaud Franck , Chopard Bastien ,   the INSIST investigators
Published: May 2023

One of the routine clinical treatments to eliminate ischemic stroke thrombi is injecting a biochemical product into the patient’s bloodstream, which breaks down the thrombi’s fibrin fibers: intravenous or intravascular thrombolysis. However, this procedure is not without risk for the patient; the worst circumstances can cause a brain hemorrhage or embolism that can be fatal. Improvement in patient management drastically reduced these risks, and patients who benefited from thrombolysis soon after the onset of the stroke have a significantly better 3-month prognosis, but treatment success is highly variable. The causes of this variability remain unclear, and it is likely that some fundamental aspects still require thorough investigations. For that reason, we conductedin vitroflow-driven fibrinolysis experiments to study pure fibrin thrombi breakdown in controlled conditions and observed that the lysis front evolved non-linearly in time. To understand these results, we developed an analytical 1D lysis model in which the thrombus is considered a porous medium. The lytic cascade is reduced to a second-order reaction involving fibrin and a surrogate pro-fibrinolytic agent. The model was able to reproduce the observed lysis evolution under the assumptions of constant fluid velocity and lysis occurring only at the front. For adding complexity, such as clot heterogeneity or complex flow conditions, we propose a 3-dimensional mesoscopic numerical model of blood flow and fibrinolysis, which validates the analytical model’s results. Such a numerical model could help us better understand the spatial evolution of the thrombi breakdown, extract the most relevant physiological parameters to lysis efficiency, and possibly explain the failure of the clinical treatment. These findings suggest that even though real-world fibrinolysis is a complex biological process, a simplified model can recover the main features of lysis evolution.
Pseudorabies virus hijacks DDX3X, initiating an addictive “mad itch” and immune suppression, to facilitate viral spread
Authors: Cronin Shane J. F. , Tejada Miguel A. , Song Ren , Laval Kathlyn , Cikes Domagoj , Ji Ming , Brai Annalaura , Stadlmann Johannes , Novatchikova Maria , Perlot Thomas , Ali Omar Hasan , Botta Lorenzo , Decker Thomas , Lazovic Jelena , Hagelkruys Astrid , Enquist Lynn , Rao Shuan , Koyuncu Orkide O. , Penninger Josef M.
Published: May 2023

Infections with defined Herpesviruses, such as Pseudorabies virus (PRV) and Varicella zoster virus (VZV) can cause neuropathic itch, referred to as “mad itch” in multiple species. The underlying mechanisms involved in neuropathic “mad itch” are poorly understood. Here, we show that PRV infections hijack the RNA helicase DDX3X in sensory neurons to facilitate anterograde transport of the virus along axons. PRV induces re-localization of DDX3X from the cell body to the axons which ultimately leads to death of the infected sensory neurons. Inducible genetic ablation ofDdx3xin sensory neurons results in neuronal death and “mad itch” in mice. This neuropathic “mad itch” is propagated through activation of the opioid system making the animals “addicted to itch”. Moreover, we show that PRV co-opts and diverts T cell development in the thymus via a sensory neuron-IL-6-hypothalamus-corticosterone stress pathway. Our data reveal how PRV, through regulation of DDX3X in sensory neurons, travels along axons and triggers neuropathic itch and immune deviations to initiate pathophysiological programs which facilitate its spread to enhance infectivity.
Ectopically expressedAirnlncRNA deposits Polycomb with a potency that rivalsXist
Authors: Trotman Jackson B. , Braceros Aki K. , Bischoff Steven R. , Murvin McKenzie M. , Boyson Samuel P. , Cherney Rachel E. , Eberhard Quinn E. , Abrash Elizabeth W. , Cowley Dale O. , Calabrese J. Mauro
Published: May 2023

We report that when expressed at similar levels from an isogenic locus, theAirnlncRNA induces Polycomb deposition with a potency that rivalsXist. However, when subject to the same degree of promoter activation,Xistis more abundant and more potent thanAirn. Our data definitively demonstrate that theAirnlncRNA is functional and suggest thatXistachieved extreme potency in part by evolving mechanisms to promote its own abundance.
CASCADE-Cas3 Enables Highly Efficient Genome Engineering inStreptomycesSpecies
Authors: Whitford Christopher M. , Gockel Peter , Faurdal David , Gren Tetiana , Sigrist Renata , Weber Tilmann
Published: May 2023

Type I CRISPR systems are widespread in bacteria and archaea. The main differences compared to more widely applied type II systems are multi-effector CASCADE needed for crRNA processing and target recognition, as well as the processive nature of the hallmark nuclease Cas3. Given the widespread nature of type I systems, the processive nature of Cas3, as well as the recombinogenic overhangs created by Cas3, we hypothesized that Cas3 would be uniquely positioned to enable efficient genome engineering in streptomycetes. Here, we report a new type I based CRISPR genome engineering tool for streptomycetes. The plasmid system, called pCRISPR-Cas3, utilizes a compact type I-C CRISPR system and enables highly efficient genome engineering. pCRISPR-Cas3, outperforms pCRISPR-Cas9 and facilitates targeted and random sized deletions, as well as substitutions of large genomic regions such as biosynthetic gene clusters. Without additional modifications, pCRISPR-Cas3 enabled genome engineering in severalStreptomycesspecies at high efficiencies.
Systematic characterization of a non-transgenic Aβ1–42amyloidosis model: synaptic plasticity and memory deficits in female and male mice
Authors: Jiménez-Herrera Raquel , Contreras Ana , Iborra-Lázaro Guillermo , Jeremic Danko , Djebari Souhail , Navarro-López Juan , Jiménez-Díaz Lydia
Published: May 2023

Background

One of the neuropathological hallmarks of Alzheimer’s disease (AD) is amyloid-β(Aβ) accumulation in the hippocampus that causes its dysfunction. This disruption includes excitatory/inhibitory imbalance, synaptic plasticity and oscillatory activity impairments, and memory deficits. Although AD prevalence is higher in women than men, the possible sex difference is scarcely explored and information from amyloidosis transgenic mice models is contradictory. Thus, given the lack of data of the early amyloidosis stages in females, the aim of this study was to systematically characterize the effect of an intracerebroventricular (icv.) injection of Aβ1–42on hippocampal-dependent memory, and on associated activity-dependent synaptic plasticity in the hippocampal CA1–CA3 synapse, in both male and female mice.

Methods

To do so, we evaluated long term potentiation (LTP) withex vivoelectrophysiological recordings and spatial (working, short- and long-term) and exploratory habituation memory using Barnes maze or open field habituation tasks respectively.

Results

We found that Aβ1–42administration impairs all forms of memory evaluated, regardless the sex, in a long-lasting manner (up to 17 days post-injection). Furthermore, LTP was inhibited at a postsynaptic level, both in males and females, and a long-term depression (LTD) was induced for the same prolonged period, which could underly memory deficits.

Conclusions

In conclusion, our results provide further evidence of the shifting of LTP/LTD threshold due to a singleicv. Aβ1-42injection, which underly cognitive deficits in early stages of AD. These long-lasting cognitive and functional alterations in males and females validate this model for the study of early amyloidosis in both sexes, thus offering a solid alternative to the inconsistence of amyloidosis transgenic mice models.
MeCP2 binds to methylated DNA independently of phase separation and heterochromatin organisation
Authors: Pantier Raphaël , Brown Megan , Han Sicheng , Paton Katie , Meek Stephen , Montavon Thomas , McHugh Toni , Kelly David A. , Hochepied Tino , Libert Claude , Jenuwein Thomas , Burdon Tom , Bird Adrian
Published: May 2023

Correlative evidence has suggested that DNA methylation promotes the formation of transcriptionally silent heterochromatin. Accordingly, the methyl-CpG binding domain protein MeCP2 is often portrayed as a constituent of heterochromatin. This interpretation has been reinforced by the use of mouse cells as an experimental system for studying the mammalian epigenome, as heterochromatin, DNA methylation and MeCP2 colocalise in prominent foci. The findings presented here revise this view. We show that focal localisation of MeCP2 in mice is independent of heterochromatin, as DNA methylation-dependent MeCP2 foci persist even when the signature heterochromatin histone mark H3K9me3 is absent and heterochromatin protein HP1 is diffuse. Contrary to the proposal that MeCP2 forms condensates at mouse heterochromatic foci via liquid-liquid phase transition, the short methyl-CpG binding domain, which lacks the disordered domains thought to be required for condensation, is sufficient to target foci in mouse cells. Importantly, we find that the formation of MeCP2 foci in mice is highly atypical, as they are indetectable in 14 out of 16 other mammalian species, including humans. Notably, MeCP2 foci are absent inMus spretuswhich can interbreed withMus musculusbut lacks its highly methylated pericentric satellite DNA repeats. We conclude that MeCP2 has no intrinsic tendency to form nuclear condensates and its localisation is independent of heterochromatin formation. Instead, the distribution of MeCP2 in the nucleus is primarily determined by global DNA methylation patterns and is typically euchromatic.
Flexible control of vocal timing inCarollia perspicillatabats enables escape from acoustic interference
Authors: Kiai Ava , Clemens Jan , Kössl Manfred , Poeppel David , Hechavarría Julio
Published: May 2023

In natural environments, background noise can degrade the integrity of acoustic signals, posing a problem for animals that rely on their vocalizations for communication and navigation. A simple behavioral strategy to combat acoustic interference would be to restrict call emissions to periods of low-amplitude or no noise. Using audio playback and computational tools for the automated detection of over 2.5 million vocalizations from groups of freely vocalizing bats, we show that bats (Carollia perspicillata) can dynamically adapt the timing of their calls to avoid acoustic jamming in both predictably and unpredictably patterned noise. This study demonstrates that bats spontaneously seek out temporal windows of opportunity for vocalizing in acoustically crowded environments, providing a mechanism for efficient echolocation and communication in cluttered acoustic landscapes.

One Sentence Summary

Bats avoid acoustic interference by rapidly adjusting the timing of vocalizations to the temporal pattern of varying noise.
A tubulin-binding protein that preferentially binds to GDP-tubulin and promotes GTP exchange
Authors: Yon Wesley J. , Ha Taekjip , Zheng Yixian , Pedersen Ross T.A.
Published: May 2023

α- and β-tubulin form heterodimers, with GTPase activity, that assemble into microtubules. Like other GTPases, the nucleotide-bound state of tubulin heterodimers controls whether the molecules are in a biologically active or inactive state. While α-tubulin in the heterodimer is constitutively bound to GTP, β-tubulin can be bound to either GDP (GDP-tubulin) or GTP (GTP-tubulin). GTP-tubulin hydrolyzes its GTP to GDP following assembly into a microtubule and, upon disassembly, must exchange its bound GDP for GTP to participate in subsequent microtubule polymerization. Tubulin dimers have been shown to exhibit rapid intrinsic nucleotide exchange in vitro, leading to a commonly accepted belief that a tubulin guanine nucleotide exchange factor (GEF) may be unnecessary in cells. Here, we use quantitative binding assays to show that BuGZ, a spindle assembly factor, binds tightly to GDP-tubulin, less tightly to GTP-tubulin, and weakly to microtubules. We further show that BuGZ promotes the incorporation of GTP into tubulin using a nucleotide exchange assay. The discovery of a tubulin GEF suggests a mechanism that may aid rapid microtubule assembly dynamics in cells.
Limited Expression ofNrf2in Neurons Across the Central Nervous System
Authors: Levings Daniel C. , Pathak Salil Saurav , Yang Yi-Mei , Slattery Matthew
Published: May 2023

Nrf2 is a broadly expressed transcription factor that regulates gene expression in response to reactive oxygen species (ROS) and oxidative stress. It is commonly referred to as a ubiquitous pathway, but this generalization overlooks work indicating that Nrf2 is essentially unexpressed in some neuronal populations. To explore whether this pattern extends throughout the central nervous system (CNS), we quantifiedNrf2expression and chromatin accessibility at theNrf2locus across multiple single cell datasets. In both the mouse and human CNS,Nrf2was repressed in almost all mature neurons, but highly expressed in non-neuronal support cells, and this pattern was robust across multiple human CNS diseases. A subset of key Nrf2 target genes, likeSlc7a11, also remained low in neurons. Thus, these data suggest that while most cells express Nrf2, with activity determined by ROS levels, neurons actively avoid Nrf2 activity by keepingNrf2expression low.
Stability of mpox (monkeypox) virus in bodily fluids and wastewater
Authors: Yinda Claude Kwe , Morris Dylan H. , Fischer Robert J , Gallogly Shane , Weishampel Zachary A. , Port Julia R. , Bushmaker Trenton , Schulz Jonathan E. , Bibby Kyle , van Doremalen Neeltje , Lloyd-Smith James O. , Munster Vincent J.
Published: May 2023

Importance

Since May 2022, human monkeypox (mpox) infections have spread rapidly outside endemic countries. On July 23, 2023, WHO declared a Public Health Emergency of international Concern because of the unprecedented global spread of mpox. Whereas there is an incomplete understanding of transmission routes, the spread of monkeypox virus (MPXV) through sexual contact networks of men who have sex with men (MSM) highlights the potential of transmission during sexual activity, either via bodily fluids or via direct contact. This research assesses the potential for MPXV to remain infectious in the environment on surfaces and in fluids under different environmental conditions.

Objective

To investigate the stability of MPXV on various surfaces, at different environmental conditions and in different bodily fluids (human blood, semen, serum, saliva, urine, and feces), and to assess decontamination of MPXV-contaminated wastewater via chlorination.

Design, Setting, and Exposures

All experiments involving viable MPXV were performed at the Rocky Mountains Laboratory under high containment conditions using MPXV strain hMPXV/USA/MA001. Infectious MPXV was quantified via plaque assay. Environmental decay rates were estimated using a Bayesian statistical model, with a Poisson likelihood for plaque counts.

Results

MPXV showed surface dependent stability, with faster decay at higher temperatures. Decay rates varied considerably depending on the medium in which virus was suspended, both overall MPXV displayed considerable environmental stability in bodily fluids and in particular proteinaceous fluids, such as blood and semen, lead to greater persistence. Wastewater chlorination was an effective decontamination technique.

Conclusions and Relevance

MPXV retains its infectivity in the environment when it is deposited in blood, semen, and serum; environmental decay is more rapid in less proteinaceous fluids, particularly once residual liquid has evaporated. The observed persistence of MPXV implies environmental contamination in healthcare setting, could serve as vehicles of transmission and dissemination in these environments. Chlorination was effective in decontamination of wastewater. Key findings and public health implications; these results suggest that MPXV can have prolonged stability in the environment and are therefore directly relevant for hospital hygiene practices to prevent nosocomial transmission.
The Regulator FleQ Post-Transcriptionally Regulates the Production of RTX Adhesins byPseudomonas fluorescens
Authors: Pastora Alexander B. , O’Toole George A.
Published: May 2023

Biofilm formation by the Gram-negative gammaproteobacteriumPseudomonas fluorescensrelies on the production of the repeat-in-toxin (RTX) adhesins LapA and MapA in the cytoplasm, secretion of these adhesins through their respective type 1 secretion systems, and retention at the cell surface. Published work has shown that retention of the adhesins occurs via a post-translational mechanism involving the cyclic-di-GMP receptor LapD and the protease LapG. However, little is known about the underlying mechanisms that regulate the production of these adhesins. Here, we demonstrate that the master regulator FleQ modulates biofilm formation by post-transcriptionally regulating the production of LapA and MapA. We find that a ΔfleQmutant has a biofilm formation defect compared to the WT strain, which is attributed in part to a decrease in LapA and MapA production, despite the ΔfleQmutant having increased levels oflapAandmapAtranscripts compared to the WT strain. Through transposon mutagenesis and subsequent genetic analysis, we found that over-stimulation of the Gac/Rsm pathway partially rescues biofilm formation in the ΔfleQmutant background. Collectively, these findings provide evidence that FleQ regulates biofilm formation by post-transcriptionally regulating the production of LapA and MapA, and that activation of the Gac/Rsm pathway can enhance biofilm formation byP. fluorescens.

Importance

Biofilm formation is a highly coordinated process that bacteria undergo to colonize a variety of surfaces. ForPseudomonas fluorescens, biofilm formation requires the production and localization of RTX adhesins to the cell surface. To date, little is known about the underlying mechanisms that regulate biofilm formation byP. fluorescens. Here, we identify FleQ as a key regulator of biofilm formation that modulates the production of LapA and MapA through a post-transcriptional mechanism. We provide further evidence implicating activation of the Gac/Rsm system in FleQ-dependent regulation of biofilm formation. Together, our findings uncover evidence for a mechanism of post-transcriptional regulation of the LapA/MapA adhesins.
Host genetic background regulates the capacity for anti-tumor antibody-dependent phagocytosis
Authors: Glassbrook James E. , Hackett Justin B. , Muñiz Maria C. , Bross Madeline , Dyson Greg , Movahhedin Nasrin , Ullrich Alexander , Gibson Heather M.
Published: May 2023

Background

Antitumor antibody, or targeted immunotherapy, has revolutionized cancer treatment and markedly improved patient outcomes. A prime example is the monoclonal antibody (mAb) trastuzumab, which targets human epidermal growth factor receptor 2 (HER2). However, like many targeted immunotherapies, only a subset of patients benefit from trastuzumab long-term. In addition to tumor-intrinsic factors, we hypothesize that host genetics may influence subsequent immune activation.

Methods

To model the human population, we produced F1 crosses of genetically heterogeneous Diversity Outbred (DO) mice with BALB/c mice (DOCF1). Distinct DOCF1 mice were orthotopically implanted with the BALB/c-syngeneic TUBO mammary tumor line, which expresses the HER2 ortholog rat neu. Treatment with anti-neu mAb clone 7.16.4 began once tumors reached ∼200 mm3. Genetic linkage and quantitative trait locus (QTL) effects analyses in R/qtl2 identified loci associated with tumor growth rates. Locus validation was performed with BALB/c F1 crosses with recombinant-inbred Collaborative Cross (CC) strains selected for therapy-associated driver genetics (CCxCF1). The respective roles of natural killer (NK) cells and macrophages were investigated by selective depletion in vivo. Ex vivo macrophage antibody-dependent phagocytosis (ADCP) assays were evaluated by confocal microscopy using 7.16.4-opsonized E2Crimson-expressing TUBO tumor cells.

Results

We observed a divergent response to anti-tumor antibody therapy in DOCF1 mice. Genetic linkage analysis detected a locus on chromosome 10 that correlates to a robust response to therapy, which was validated in CCxCF1 models. Single-cell RNA sequencing of tumors from responder and non-responder models identified key differences in tumor immune infiltrate composition, particularly within macrophage (Mφ) subsets. This is further supported byex vivoanalysis showing Mφ ADCP capacity correlates toin vivotreatment outcomes in both DOCF1 and CCxCF1 models.

Conclusions

Host genetics play a key regulatory role in targeted immunotherapy outcomes, and putative causal genes are identified in murine chromosome 10 which may govern Mφ function during ADCP.
Brief oxygen exposure after traumatic brain injury speeds recovery and promotes adaptive chronic endoplasmic reticulum stress responses
Authors: Torrens Jordyn N. , Hetzer Shelby M. , Evanson Nathan K.
Published: May 2023

Traumatic brain injury (TBI) is a major public health concern particularly in adolescents who have a higher mortality and incidence of visual pathway injury compared to adult patients. Likewise, we have found disparities between adult and adolescent TBI outcomes in rodents. Most interestingly, adolescents suffer a prolonged apneic period immediately post injury leading to higher mortality; so, we implemented a brief oxygen exposure paradigm to circumvent this increased mortality. Adolescent male mice experienced a closed-head weight-drop TBI then were exposed to 100% O2until normal breathing returned or recovered in room air. We followed mice for 7- and 30-days and assessed their optokinetic response; retinal ganglion cell loss; axonal degeneration; glial reactivity; and retinal ER stress protein levels. O2reduced adolescent mortality by 40%, improved post-injury visual acuity, and reduced axonal degeneration and gliosis in optic projection regions. ER stress protein expression was altered in injured mice, and mice given O2utilized different ER-stress pathways in a time dependent manner. Finally, O2exposure may be mediating these ER stress responses through regulation of the redox-sensitive ER folding protein ERO1α, which has been linked to a reduction in the toxic effects of free radicals in other animal models of ER stress.
CpG island turnover events predict evolutionary changes in enhancer activity
Authors: Kocher Acadia A. , Dutrow Emily V. , Uebbing Severin , Yim Kristina M. , Rosales Larios María F. , Baumgartner Marybeth , Nottoli Timothy , Noonan James P.
Published: May 2023

Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. Here we show that turnover of CpG islands (CGIs), which contribute to enhancer activation, is broadly associated with changes in enhancer activity across mammals, including humans. We integrated maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and found that CGI content in enhancers was strongly associated with increased histone modification levels. CGIs showed widespread turnover across species and species-specific CGIs were strongly enriched for enhancers exhibiting species-specific activity across all tissues and species we examined. Genes associated with enhancers with species-specific CGIs showed concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
Building synthetic chromosomes from natural DNA
Authors: Coradini Alessandro L.V. , Ne Ville Christopher , Krieger Zachary A. , Roemer Joshua , Hull Cara , Yang Shawn , Lusk Daniel T. , Ehrenreich Ian M.
Published: May 2023

De novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning,Reprogramming, andAssemblingTiledNaturalGenomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We used CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment revealed that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.
Healthcare resource utilisation and costs of hospitalisation and primary care among adults with COVID-19 in England: a population-based cohort study
Authors: Yang Jingyan , Andersen Kathleen M. , Rai Kiran K. , Tritton Theo , Mugwagwa Tendai , Reimbaeva Maya , Tsang Carmen , McGrath Leah J. , Payne Poppy , Backhouse Bethany , Mendes Diana , Butfield Rebecca , Naicker Kevin , Araghi Mary , Wood Robert , Nguyen Jennifer L.
Published: May 2023

Objectives

To quantify healthcare resource utilisation (HCRU) and costs to the National Health Service (NHS) associated with acute COVID-19 in adults in England.

Design

Population-based retrospective cohort study, using Clinical Practice Research Datalink (CPRD) Aurum primary care electronic medical records linked when available to Hospital Episode Statistics (HES) secondary care administrative data.

Setting

Patients registered to primary care practices in England.

Population

1,706,368 adults with a positive SARS-CoV-2 PCR or antigen test from August 2020 to January 2022 were included; 13,105 within the hospitalised cohort indexed between August 2020 and March 2021, and 1,693,263 within the primary care cohort indexed between August 2020 and January 2022.

Main outcome measures

Primary and secondary care HCRU and associated costs during the acute phase of COVID-19 (≤4 weeks following positive test), stratified by age group, risk of severe COVID-19 and immunocompromised status.

Results

Among the hospitalised cohort, average total length of stay, as well as in critical care wards, was longer in older adults. Median healthcare cost per hospitalisation was higher in those aged 75 – 84 (£8,942) and ≧85 years (£8,835) than in those aged <50 years (£7,703). Whilst few (6.0%) patients in critical care required mechanical ventilation, its use was higher in older adults (50 – 74 years: 8.3%; <50 years: 4.3%). HCRU and associated costs were often greater in those at higher risk of severe COVID-19 when compared to the overall cohort, although minimal differences in HCRU were found across the three different high-risk definitions implemented. Among the primary care cohort, GP or nurse consultations were more frequent among older adults and the immunocompromised.

Conclusions

COVID-19 related hospitalisations in older adults, particularly critical care admissions, were the primary drivers of high resource use of COVID-19 in England. These findings may inform health policy decisions and resource allocation in the prevention and management of COVID-19.
A Retrospective Study to Determine the Impact of Psychedelic Therapy for Dimensional Measures of Wellness: A Quantitative Analysis
Authors: Di Virgilio Victoria , Minerbi Amir , Deol Jagpaul Kaur , Aggerwal Salena , Safi Toufik , Gupta Gaurav
Published: May 2023

Background

The World Health Organization (WHO) defines wellness as the optimal state of health of individuals and groups. No study to date has identified the impact of psychedelic medicines on optimizing wellness using a dimensional approach. Using this approach, treatment effects can be measured more broadly using a composite score of participants’ global perceptions of change for pain, function, and mood scores. Given the precedence in previous work for retrospective studies of participants’ self-medicating with these substances, the nature of this study design allows for a safe way to develop further evidence in this area of care, with wellness as the broad indication.

Methods

65 civilian or military veterans above the age of 18, self-identifying as having used psychedelic medicines for non-recreational purposes in the last 3 years were recruited. Participants completed the following standardized questionnaires: Patient Global Impression of Change (PGIC) scale, Pain, Enjoyment of Life and General Activity (PEG) scale, Anxiety and Depression scale (ADS), and Disability Index (DI) scale. The analysis focused on reported PGIC outcomes and correlations between subscales. Given the nature of the study, a comparison to the baseline could not be made.

Results

On average, participants reported improvement in all domains (pain, mental health, function, and overall quality of life), regardless of the medicine. Perceived improvement was highest in mental health and overall quality of life, and lowest in pain. Kendall correlation showed a highly significant association between the perceived changes in all domains. Correlation coefficients were highest between the perceived change in function, quality of life, and mental health.

Discussion

The use of various psychedelic medicines may be associated with a broad range of changes that could help clarify the mechanism of how they impact wellness in the future. Pain, mental health, function, and overall quality of life accordingly improved after the use of these medicines. Minor differences between the drugs were not found as significant, indicating that the perceived benefits seemed to be specific to the psychedelic class. Numerous limitations exist to this type of study which was relatively small in size, retrospective and anonymous in nature.

Conclusion

The wellness of individuals or groups is not simply an absence of disease, symptoms, or impairments. Instead, it is an outcome that is shaped by a myriad of personal characteristics, psychophysiology, and choices, expressed throughout one’s lifespan, unfolding in dynamic interaction with a complicated sociocultural and physical environment.
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation
Authors: Pikkupeura Laura M. , Bressan Raul B. , Guiu Jordi , Chen Yun , Maimets Martti , Mayer Daniela , Schweiger Pawel J. , Hansen Stine L. , Maciag Grzegorz J. , Larsen Hjalte L. , Lõhmussaar Kadi , Pedersen Marianne Terndrup , Teves Joji M. Yap , Bornholdt Jette , Benes Vladimir , Sandelin Albin , Jensen Kim B.
Published: May 2023

During intestinal organogenesis, equipotent epithelial progenitors mature into phenotypically distinct stem cells that are responsible for life-long maintenance of the tissue. While the morphological changes associated with the transition are well-characterized, the molecular mechanisms underpinning the maturation process are not fully understood. Here, we leverage intestinal organoid cultures to profile transcriptional, chromatin accessibility, DNA methylation and 3D chromatin conformation landscapes defining fetal and adult epithelial cells. We observed prominent differences in gene expression and enhancer activity, accompanied by changes in 3D organization and local changes in DNA accessibility and methylation, between the two cellular states. Using integrative analyses, we identified sustained YAP transcriptional activity as a major gatekeeper of the immature fetal state. We found the YAP-associated transcriptional network to be regulated at various levels of chromatin organization, and likely to be coordinated by changes in extracellular matrix composition. Altogether, our work highlights the value of unbiased profiling of regulatory landscapes for the identification of key mechanisms underlying tissue maturation.
A population intrinsic timer controlsHoxgene expression and cell dispersion during progenitor addition to the body axis
Authors: Busby Lara , Nájera Guillermo Serrano , Steventon Ben
Published: May 2023

During embryonic development, the timing of events at the cellular level must be coordinated across multiple length scales to ensure the formation of a well-proportioned body plan. This is clear during somitogenesis, where the progenitors must be allocated to the axis over time whilst maintaining a progenitor population for continued elaboration of the body plan. However, the relative importance of intrinsic and extrinsic signals in timing progenitor addition at the single cell level is not yet understood. Heterochronic grafts from older to younger embryos have suggested a level of intrinsic timing whereby later staged cells contribute to more posterior portions of the axis. To determine the precise step at which cells are delayed, we performed single-cell transcriptomic analysis on heterochronic grafts of somite progenitors in the chicken embryo. This revealed a previously undescribed cell state within which heterochronic grafted cells are stalled, post-ingression through the primitive streak. The delayed exit of older cells from this state correlates with expression of posteriorHoxgenes. Using grafting and explant culture, we find that bothHoxgene expression and the migratory capabilities of progenitor populations are intrinsically regulated at the population level. Therefore, we demonstrate that cell dispersion is controlled by a population intrinsic timer to control progenitor addition to the presomitic mesoderm.
A BubR1-independent pathway for CENP-E targeting to the outer corona of kinetochores
Authors: Legal Thibault , Paterson Calum , Gluszek Agata , Davies Owen R. , Welburn Julie P.I.
Published: May 2023

For chromosome segregation to take place, unattached kinetochores expand in early mitosis, forming a fibrous structure called the fibrous corona that is captured by microtubules. The corona is assembled from the RZZ complex, Spindly, CENP-E and the Mad1/Mad2 spindle assembly checkpoint proteins. CENP-E aligns chromosomes along the mitotic spindle by moving them to the plus ends of microtubules. Here, we show that CENP-E is recruited to the outer corona independently of BubR1 in a dynein-dependent fashion. We determine the structure of this domain and show that a conserved loop is essential for CENP-E targeting to the outer corona. We show that both domains are essential for CENP-E recruitment to unattached kinetochores. We also report that the kinetochore-targeting domain of CENP-E contributes to the recruitment of the RZZ complex, Mad1 and Spindly, providing a feedback loop to assemble the outer corona. In this study, we propose that CENP-E uses 2 pathways to target to the kinetochore, which allows it to optimize kinetochore capture by microtubules for chromosome alignment and mitotic progression.
The action of physiological and synthetic steroids on the calcium channel CatSper in human sperm
Authors: Wehrli Lydia , Galdadas Ioannis , Voirol Lionel , Smieško Martin , Cambet Yves , Jaquet Vincent , Guerrier Stéphane , Gervasio Francesco Luigi , Nef Serge , Rahban Rita
Published: May 2023

The sperm-specific channel CatSper (cation channel ofsperm) controls the intracellular Ca2+concentration ([Ca2+]i) and plays an essential role in sperm function. It is mainly activated by the steroid progesterone (P4) but is also promiscuously activated by a wide range of synthetic and physiological compounds. These compounds include diverse steroids whose action on the channel is so far still controversial. To investigate the effect of these compounds on CatSper and sperm function, we developed a high-throughput-screening (HTS) assay to measure changes in [Ca2+]iin human sperm and screened 1,280 approved and off-patent drugs including 90 steroids from the Prestwick chemical library. More than half of the steroids tested (53%) induced an increase in [Ca2+]iand reduced the P4-induced Ca2+influx in human sperm in a dose-dependent manner. Ten of the most potent steroids (activating and inhibiting) were selected for a detailed analysis of their action on CatSper and their ability to act on sperm motility, acrosomal exocytosis (AR), and penetration in viscous media. We found that these steroids show an inhibitory effect on P4 but not on prostaglandin E1-induced CatSper activation, suggesting that they compete for the same binding site as P4. Pregnenolone, dydrogesterone, epiandrosterone, nandrolone, and dehydroepiandrosterone acetate (DHEA) were found to activate CatSper at physiological concentrations. Stanozolol, epiandrosterone, and pregnenolone induced AR similarly to P4, whereas stanozolol and estropipate induced an increase in sperm penetration into viscous medium. Furthermore, using a hybrid approach integrating pharmacophore analysis and statistical modelling, we were able to screenin silicofor steroids that can activate the channel and define the physicochemical and structural properties required for a steroid to exhibit agonist activity against CatSper. Overall, our results indicate that not only physiological but also synthetic steroids can modulate the activity of CatSper with varying potency and affect human sperm functionsin vitro.
Gaps and complex structurally variant loci in phased genome assemblies
Authors: Porubsky David , Vollger Mitchell R. , Harvey William T. , Rozanski Allison N. , Ebert Peter , Hickey Glenn , Hasenfeld Patrick , Sanders Ashley D. , Stober Catherine ,   Human Pangenome Reference Consortium, Korbel Jan O. , Paten Benedict , Marschall Tobias , Eichler Evan E.
Published: May 2023

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6–7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.
A familialSAMD9variant present in pediatric myelodysplastic syndrome
Authors: Rahim Mahvish Q. , Rahrig April , Overholt Kathleen , Conboy Erin , Czader Magdalena , Saraf Amanda June
Published: May 2023

Myelodysplastic syndrome (MDS) is a rare pediatric diagnosis characterized by ineffective hematopoiesis with potential to evolve into acute myelogenous leukemia (AML). In this report, we describe a unique case of a 17-yr-old female with an aggressive course of MDS with excess blasts who was found to have monosomy 7 and aSAMD9germline variant, which has not previously been associated with a MDS phenotype. This case of MDS was extremely rapidly progressing, showing resistance to chemotherapy and stem cell transplant, unfortunately resulting in patient death. It is imperative to further investigate this rare variant to aid in the future care of patients with this variant.
From a short-term study abroad student to a future expatriate – contrasting the effects of social support from the host-country nationals, sociocultural adaptation, and acculturation attitude
Authors: Kingminghae Worapinya , Lin Yi
Published: May 2023

Purpose

The purpose of this study is to explore how three experiential factors – perceived social support from host-country nationals (HCNs), adaptation difficulties, and attitude towards assimilating into the host culture and society – influence the generation of worthwhile feelings and the intention to pursue expatriate career opportunities in the host country among short-term studying abroad (STSA) students.

Design/methodology/approach

This study used data from a survey of 297 Thai students who studied in Chinese universities between 2015 and 2019. A bivariate probit model was applied due to its ability to account for the potential correlation of errors between the two binary outcome variables: worthwhileness and aspiration for expatriate careers.

Findings

Adaptation difficulties reported by students negatively impacted their willingness to work in the host country, but did not diminish their perception of the sojourn as worthwhile. Satisfaction with social support from HCNs was found to not only enhance the worthwhileness of the sojourn but also inspire students' expatriate career intentions in the host country. The study also found that while willingness to assimilate into the host culture and society primarily enhanced the worthwhileness of the trip, its effect on students' willingness to consider working in the host country was relatively weak, compared with the effect of social support from HCNs.

Research limitations/implications

The generalizability of the findings from this study may be limited to country pairs that are geographically and culturally similar.

Originality/value

Although it is commonly believed that STSA programs help inspire students to develop aspirations for international careers or lifestyles, the specific roles of various factors in their experiences abroad have not been sufficiently studied. This study aims to clarify the different effects between social support received, adaptation difficulties experienced, and inner acculturation attitudes on both the evaluation of the trip itself and the long-term life goals of students participating in STSA programs.
Closed-form and technology independent phase noise relation for LC oscillators
Authors: Moradnezhad Mehrdad , Miar-Naimi Hossein
Published: May 2023

Purpose

The purpose of this paper is to find a closed relation for the phase noise of LC oscillators.

Design/methodology/approach

The governing equation of oscillators is generally a stochastic nonlinear differential equation. In this paper, a closed relation for the phase noise of LC oscillators was obtained by approximating the I–V characteristic of the oscillator with third-degree polynomials and analyzing its differential equation.

Findings

This relation expresses phase noise directly in terms of circuit parameters, including the sizes of the transistors and the bias. Next, for evaluation, the phase noise of the cross-coupled oscillator without tail current was calculated with the proposed model. In this approach, the obtained equations are expressed independently of technology by combining the obtained phase noise relation and gm/ID method.

Originality/value

A technology-independent method using the gm/ID method and the closed relationship is provided to calculate phase noise.