bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of methods to measure the forces at the rear suspension of a race car during racetrack driving
Authors: Cortivo D , Dindo L , Vendramin M , Meneghetti G
Published: January 2022

The forces generated by the tyres of a vehicle are responsible for the maximum achievable performance for a race car. In this work, a geometric matrix method combined with a sensitivity matrix method has been applied to a rear multi-link suspension of a rear-wheel-drive race car to estimate the tyre forces from the measurement of the loads acting on the suspension arms. The geometric matrix method calculates the wheel forces from the equilibrium of the wheel assembly, thus involving all reaction forces exchanged with the suspension arms. The reaction forces have been measured through the application of axial strain gauge bridges on the link arms; however, the lower arm has a complex geometry and exchanges multi-axial forces with the upright, therefore a sensitivity matrix method has been implemented. The strain gauges positions have been identified with FE analyses and after installing the sensors, the calibration of the entire suspension assembly has been performed in a dedicated test rig where known forces at the ideal contact point between the wheel and the ground can be applied. After the calibration and validation in the laboratory, the instrumented suspension has been installed in a race vehicle and multiple racetrack acquisitions have been successfully performed.
Mechanistic convergence across initiation sites for RAN translation in fragile X associated tremor ataxia syndrome
Authors: Zhang Yuan , Glineburg M Rebecca , Basrur Venkatesha , Conlon Kevin , Wright Shannon E , Krans Amy , Hall Deborah A , Todd Peter K
Published: January 2022

Repeat associated non-AUG (RAN) translation of CGG repeats in the 5′UTR of FMR1 produces toxic proteins that contribute to fragile X-associated tremor/ataxia syndrome (FXTAS) pathogenesis. The most abundant RAN product, FMRpolyG, initiates predominantly at an ACG upstream of the repeat. Accurate FMRpolyG measurements in FXTAS patients are lacking. We used data-dependent acquisition and parallel reaction monitoring (PRM) mass spectrometry coupled with stable isotope labeled standard peptides to identify signature FMRpolyG fragments in patient samples. Following immunoprecipitation, PRM detected FMRpolyG signature peptides in transfected cells, and FXTAS tissues and cells, but not in controls. We identified two amino-terminal peptides: an ACG-initiated Ac-MEAPLPGGVR and a GUG-initiated Ac-TEAPLPGGVR, as well as evidence for RAN translation initiation within the CGG repeat itself in two reading frames. Initiation at all sites increased following cellular stress, decreased following eIF1 overexpression and was eIF4A and M7G cap-dependent. These data demonstrate that FMRpolyG is quantifiable in human samples and FMR1 RAN translation initiates via similar mechanisms for near-cognate codons and within the repeat through processes dependent on available initiation factors and cellular environment.
H and HL synergistically regulate jasmonate-triggered trichome formation in tomato
Authors: Hua Bing , Chang Jiang , Han Xiaoqian , Xu Zhijing , Hu Shourong , Li Shuang , Wang Renyin , Yang Liling , Yang Meina , Wu Shasha , Shen Jingyuan , Yu Xiaomin , Wu Shuang
Published: January 2022

The development of trichomes, which protect plants against herbivores, is affected by various stresses. In tomato, previous studies showed that stress-triggered jasmonic acid (JA) signaling influences trichome formation, but the underlying mechanism is not fully resolved. Here, we found that two C2H2 zinc finger proteins synergistically regulate JA-induced trichome formation in tomato. The naturally occurring mutations in the H gene and its close homolog H-like in a spontaneous mutant, LA3172, cause severely affected trichome development. Compared with the respective single mutant, the h/hl double mutant displayed more severe trichome defects in all tissues. Despite their partially redundant function, the H and HL genes regulate trichome formation in a spatially distinct manner, with HL more involved in hypocotyls and leaves while H is more involved in stems and sepals. Furthermore, the activity of H/HL is essential for JA-triggered trichome formation. The JA signaling inhibitor SlJAZ2 represses the activity of H and HL via physical interaction, resulting in the activation of THM1, a negative regulator of trichome formation. Our results provide novel insight into the mechanism of trichome formation in response to stress-induced JA signaling in tomato.
Getting to the Root of US Healthcare Injustices through Morrison’s Root Workers
Authors: Anatol Giselle Liza
Published: January 2022

Although a number of scholars have tackled the figure of the Black folk-healer in Toni Morrison’s novels, the character deserves greater attention in the present moment for the insights she provides into two contemporary catastrophes: the coronavirus pandemic and the structural racism that precipitates rampant violence against brown-skinned people in the United States. Beginning with M’Dear, the elderly woman who is brought in to treat Cholly’s Aunt Jimmy in The Bluest Eye (1970), I survey descriptions of several root workers, hoodoo practitioners, and midwives in Morrison’s fiction, including Ajax’s mother in Sula (1973) and Milkman’s aunt Pilate in Song of Solomon (1977). Morrison’s portraits of these women and their communities capture the endurance of African folk customs, the undervalued knowledge of aged members of society, and a sense of Black women’s strength beyond that of the physical, laboring, or hypersexual body. The fictional experiences of Morrison’s healers also alert readers to the very real injustices that have historically impeded the successes of African Americans—and continue to hamper them, as has been exposed during the COVID-19 crisis and public outrages over police brutality. These injustices include inequities in lifelong earning potential, education, housing, and access to healthcare. Paying closer attention to the Nobel Laureate’s root-working women makes her novels more than simply “transformative” and “empowering” for individual readers; analyzing these figures allows one to unearth important critiques of medical bias and other forms of discrimination against marginalized members of society—disparities that must be dismantled in the push for social change.
Public Support for Cigarette Pack Pictorial Health Warnings Among US Adults: A Cross-sectional Analysis of the 2020 Health Information National Trends Survey
Authors: Kaufman Annette R , D’Angelo Heather , Gaysynsky Anna , Seidenberg Andrew B , Vollinger Robert E , Blake Kelly D
Published: January 2022

Introduction

The US Food and Drug Administration issued a final rule requiring new warnings for cigarette packages and advertisements. This study examines population-level characteristics of support for—versus neutrality or opposition toward—cigarette pack warnings that use text and images to portray the negative health effects of smoking.

Methods

We used nationally representative cross-sectional data of US adults age 18 and older from the 2020 Health Information National Trends Survey (n = 3865). Frequencies and weighted proportions were calculated for neutrality toward, opposition to, and support for pictorial warnings across sociodemographics and other predictors. Weighted, multivariable logistic regression examined predictors of being neutral or opposed versus supportive of pictorial warnings.

Results

In 2020, an estimated 69.9% of US adults supported pictorial warnings, 9.1% opposed, and 20.9% neither supported nor opposed them. In fully adjusted models, current smokers had almost twice the odds of being neutral or opposed to pictorial warnings as never smokers (odds ratio [OR] = 1.99, confidence interval [CI] 1.12, 3.52). Adults 75 years and older (vs. 18–34) (OR = 0.55, CI 0.33, 0.94) and those with children under 18 in their household (vs. no children) (OR = 0.67, CI 0.46, 0.98) were less likely to be neutral or opposed.

Conclusions

In advance of the Food and Drug Administration’s implementation of pictorial warnings on cigarette packages, nearly 70% of American adults support this policy. Disseminating information about the effectiveness of pictorial warnings may further strengthen support among current smokers who are less supportive than never smokers. Furthermore, framing messages around the benefits of pictorial warnings for protecting youth may increase public support.

Implications

While public support for pictorial warnings on cigarette packages is high in the United States, it may increase further after policy implementation and be strengthened by utilizing information campaigns that convey the evidence that pictorial warnings are an effective public health strategy.
“New normal” at work in a post-COVID world: work–life balance and labor markets
Authors: Vyas Lina
Published: January 2022

The coronavirus pandemic has interrupted labor markets, triggering massive and instant series of experimentations with flexible work arrangements, and new relationships to centralized working environments. These approaches have laid the basis for the “new normal,” likely extending into the organization of work in the post-pandemic era. These new arrangements, especially flexible work arrangements, have challenged traditional relationships with employees and employers, work time and working hours, the work–life balance (WLB), and the relationship of individuals to work. This paper investigates how labor markets have been interrupted due to the pandemic, focusing especially on manual (blue-collar) and nonmanual (white-collar) work and the future of the WLB, along with exploring the projected deviations that are driving a foreseeable future policy revolution in work and employment. This paper argues that although hybrid and remote working would be more popular in the post-pandemic for nonmanual work, it will not be “one size fits all” solution. Traditional work practices will remain, and offices will not completely disappear. Manual labor will continue current work practices with increased demands. Employers’ attention to employees’ WLB in the new normal will target employees’ motivation and achieving better WLB. These trends for the labor market and WLB are classified into three categories—those that are predicated on changes that were already underway but were accelerated with arrival of the pandemic (“acceleration”); those that represent normalization of what were once considered avant-garde ways of work (“normalization”); and those that represent modification or alteration of pre-pandemic set-up (“remodelling”).
Essential Roles of Cupredoxin Family Proteins in Soybean Cyst Nematode Resistance
Authors: Zhang Lei , Zeng Qian , Zhu Qun , Tan Yuanhua , Guo Xiaoli
Published: January 2022

Soybean cyst nematode (SCN, Heterodera glycines), one of the most devastating soybean pathogens, causes a significant yield loss in soybean production. One of the most effective ways to manage SCN is to grow resistant cultivars. Therefore, comparative study using resistant and susceptible soybean cultivars provides a powerful tool to identify new genes involved in soybean SCN resistance. In the present study, a transcriptome analysis was carried out using both the resistant (PI88788) and susceptible (Williams 82) soybean cultivars to characterize the responses to nematode infection. Various defense-related genes and different pathways involved in nematode resistance were recognized as being highly expressed in resistant cultivar. Promoter-GUS analysis was conducted to monitor the spatial expression pattern of the genes highly induced by nematode infection. Two nematode-inducible promoters for Glyma.05g147000 (encoding caffeoyl-CoA O-methyltransferase) and Glyma.06g036700 (encoding cupredoxin superfamily protein) were characterized, and the promoters could efficiently drive the expression of known nematode resistance genes (α-SNAPRhg1HC or GmSHMT) to affect soybean SCN resistance. Interestingly, expression of the cupredoxin family genes was upregulated not only by SCN, but also by jasmonic acid treatment. DNA sequence analysis identified that a conserved motif (GGTGCATG) with high similarity to SCNbox1 and GC-rich element is enriched in their promoter regions, suggesting its potential to serve as a nematode-responsive regulatory element. Overexpression of Glyma.06g036700 significantly enhanced soybean resistance to cyst nematode. Overall, our findings not only highlight the essential role of cupredoxin family genes in SCN resistance, but also offer potential functional tools to develop nematode resistance in crops.
Monocyclic Components and Photosynthetic Damage Caused by Myrtle Rust in Guava Leaves
Authors: Gonçalves Manoel Penachio , Nogueira Júnior Antonio Fernandes , Ribeiro Rafael Vasconcelos , Amorim Lilian
Published: January 2022

Austropuccinia psidii, the causal agent of myrtle rust, was, for many years, restricted to the Americas, but since reaching Hawaii in 2005, the pathogen has expanded its global range exponentially. In Brazil, myrtle rust is the main fungal disease in guava plants. Despite this, there are few studies on guava rust epidemiology. The objectives of this study were to quantify the monocyclic components of rust and to evaluate the photosynthetic damage caused by A. psidii in young and old leaves of ‘Paluma’ guava. The monocyclic components of guava rust and gas exchange in healthy or inoculated (105 ml–1 urediniospores of A. psidii) leaves were quantified over time. Additionally, young leaves were inoculated with varying concentrations of A. psidii inoculum, and leaf gas exchange and chlorophyll fluorescence were measured at 25 days postinoculation. The relationship between the relative CO2 assimilation of a diseased leaf (Px) and a healthy leaf (Po) is related to disease severity (x) by Px/Po = (1 – x)β. The density of lesions, disease severity, and urediniospore production were high in young leaves, averaging 58 lesions cm–2, 50% leaf area diseased, and 2.5 × 104 urediniospores per lesion, respectively. Rust symptoms were not observed in old leaves, and resistance to infection did not cause any photosynthetic cost to these leaves. On young leaves, β was 2.13, indicating a reduction on CO2 assimilation at green tissues from symptomatic leaves. Our data revealed that photosynthesis reduction in diseased guava leaves was caused by biochemical and photochemical damage rather than by stomatal limitation.
Exposure to 1800 MHz LTE electromagnetic fields under proinflammatory conditions decreases the response strength and increases the acoustic threshold of auditory cortical neurons
Authors: Souffi Samira , Lameth Julie , Gaucher Quentin , Arnaud-Cormos Délia , Lévêque Philippe , Edeline Jean-Marc , Mallat Michel
Published: January 2022

Increased needs in mobile phone communications have raised successive generations (G) of wireless technologies, which could differentially affect biological systems. We have assessed how a single 2h head-only exposure to a 4G long term evolution (LTE)-1800 MHz electromagnetic field (EMF) impacts on the microglial space coverage and the electrophysiological neuronal activity in the primary auditory cortex (ACx) in rats submitted to an acute neuroinflammation induced by lipopolysaccharide. The mean specific absorption rate in the ACx was 0.5 W/kg. Multiunit recording revealed that LTE-EMF triggered reduction in the response strength to pure tones and to natural vocalizations, together with an increase in acoustic threshold in the low and medium frequencies. Iba1 immunohistochemistry showed no change in the area covered by microglia cell bodies and processes. In healthy rats, the same LTE-exposure induced no change in response strength and acoustic threshold. Our data indicate that an acute neuroinflammation sensitize neuronal responses to LTE-EMF, which leads to an altered processing of acoustic stimuli in the ACx.
ELF5 is a respiratory epithelial cell-specific risk gene for severe COVID-19
Authors: Pietzner Maik , Chua Robert Lorenz , Wheeler Eleanor , Jechow Katharina , Radbruch Helena , Trump Saskia , Heidecker Bettina , Heppner Frank L. , Eils Roland , Mall Marcus A. , Sander Leif-Erik , Lehmann Irina , Lukassen Sören , Wareham Nick , Conrad Christian , Langenberg Claudia
Published: January 2022

Despite two years of intense global research activity, host genetic factors that predispose to a poorer prognosis and severe course of COVID-19 infection remain poorly understood. Here, we identified eight candidate protein mediators of COVID-19 outcomes by establishing a shared genetic architecture at protein-coding loci using large-scale human genetic studies. The transcription factor ELF5 (ELF5) showed robust and directionally consistent associations across different outcome definitions, including a >4-fold higher risk (odds ratio: 4.85; 95%-CI: 2.65-8.89; p-value<3.1×10−7) for severe COVID-19 per 1 s.d. higher genetically predicted plasma ELF5. We show that ELF5 is specifically expressed in epithelial cells of the respiratory system, such as secretory and alveolar type 2 cells, using single-cell RNA sequencing and immunohistochemistry. These cells are also likely targets of SARS-CoV-2 by colocalisation with key host factors, including ACE2 and TMPRSS2. We also observed a 25% reduced risk of severe COVID-19 per 1 s.d. higher genetically predicted plasma G-CSF, a finding corroborated by a clinical trial of recombinant human G-CSF in COVID-19 patients with lymphopenia reporting a lower number of patients developing critical illness and death. In summary, large-scale human genetic studies together with gene expression at single-cell resolution highlight ELF5 as a novel risk gene for COVID-19 prognosis, supporting a role of epithelial cells of the respiratory system in the adverse host response to SARS-CoV-2.
Robust, long-term video EEG monitoring in a porcine model of post-traumatic epilepsy
Authors: Martinez-Ramirez Luis , Slate Andrea , Price George , Duhaime Ann-Christine , Staley Kevin , Costine-Bartell Beth A.
Published: January 2022

To date, post-traumatic epilepsy (PTE) research in large animal models has been limited. Recent advances in neocortical microscopy have made possible new insights into neocortical PTE. However, it is very difficult to engender convincing neocortical PTE in rodents. Thus, large animal models that develop neocortical PTE may provide useful insights that also can be more comparable to human patients. Because gyrencephalic species have prolonged latent periods, long-term video EEG recording is required. Here, we report a fully subcutaneous EEG implant with synchronized video in freely ambulatory swine for up to 14 months during epileptogenesis following bilateral cortical impact injuries or sham surgery The advantages of this system include the availability of a commercially available system that is simple to install, a low failure rate after surgery for EEG implantation, radiotelemetry that enables continuous monitoring of freely ambulating animals, excellent synchronization to video to EEG, and a robust signal to noise ratio. The disadvantages of this system in this species and age are the accretion of skull bone which entirely embedded a subset of skull screws and EEG electrodes, and the inability to rearrange the EEG electrode array. These disadvantages may be overcome by splicing a subdural electrode strip to the electrode leads so that skull growth is less likely to interfere with long-term signal capture and by placing two implants for a more extensive montage. This commercially available system in this bilateral cortical impact swine model may be useful to a wide range of investigators studying epileptogenesis in PTE.

Significance

Post-traumatic epilepsy (PTE) is a cause of significant morbidity after traumatic brain injury (TBI) and is often drug-resistant. Robust, informative animal models would greatly facilitate PTE research. Ideally, this biofidelic model of PTE would utilize a species that approximates human brain anatomy, brain size, glial populations, and inflammatory pathways. An ideal model would also incorporate feasible methods for long-term video EEG recording required to quantify seizure activity. Here, we describe the first model of PTE in swine and describe a method for robust long-term video EEG monitoring for up to 14 months post-TBI. The relatively easy “out-of-the-box” radiotelemetry system and surgical techniques described here will be adaptable by a wide array of investigators studying the pathogenesis and treatment of PTE.
Combiroc: when ‘less is more’ in bulk and single cell marker signatures
Authors: Ferrari I. , Mazzara S. , Crosti M. , Abrignani S. , Grifantini R. , Bombaci M. , Rossi R.L.
Published: January 2022

Here we present thecombirocR package, for signatures refinement in high throughput omics. Based on a ROC-driven marker selection, it can be used to find powerful smaller sub-signatures from scRNAseq experiments and to annotate cells using fewer markers. Trained on PBMC dataset, combiroc found NK marker combinations with high cell-discriminating power, in agreement with human protein atlas and that were validated both computationally and experimentally on independent datasets.
Cell-Type Specific Profiling of Histone Post-Translational Modifications in the Adult Mouse Striatum
Authors: Carpenter Marco D. , Fischer Delaney K. , Zhang Shuo , Bond Allison M , Czarnecki Kyle S. , Woolf Morgan T. , Song Hongjun , Heller Elizabeth A.
Published: January 2022

Histone post-translational modifications (hPTMs) regulate gene expression via changes in chromatin accessibility and transcription factor recruitment. At a given locus, the coordinated enrichment of several distinct hPTMs regulate gene expression in response to external stimuli. However, neuronal hPTMs have been primarily characterized in bulk brain tissue and/or tissue pooled across subjects. This obscures both cell-type and individual variability, features essential to understand individual susceptibility to psychiatric disease. To address this limitation, we optimized a hybrid protocol, ICuRuS, to profile both activating and repressive hPTMs in neuronal subtypes from a single mouse. We report here profiling of striatal medium spiny neuron (MSN) subtypes, genetically defined by expression of Adenosine 2a Receptor (A2a) or Dopamine Receptor D1 (D1), which differentially regulate reward processing and pathophysiology. Using ICuRuS, we defined genome-wide, A2a- or D1-specific combinatorial hPTM profiles, and discovered regulatory epigenomic features at genes implicated in neurobiological function and disease.
Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests
Authors: Rasmussen David A. , Guo Fangfang
Published: January 2022

In the presence of recombination individuals may inherit different regions of their genome from different ancestors, resulting in a mosaic of phylogenetic histories across their genome. Ancestral recombination graphs (ARGs) can capture how phylogenetic relationships vary across the genome due to recombination, but reconstructing ARGs from genomic sequence data is notoriously difficult. Here we present a method for reconciling discordant phylogenetic trees and reconstructing ARGs using maximum agreement forests (MAFs). Given two discordant trees, a MAF identifies a set of topologically concordant subtrees present in both trees. We show how discordant trees can be reconciled through their MAF in a way that retains discordances strongly supported by sequence data while eliminating conflicts likely attributable to phylogenetic noise. We further show how MAFs and our reconciliation approach can be combined to select a path of local trees across the genome that maximizes the likelihood of the genomic sequence data, minimizes discordance between neighboring local trees, and identifies the recombination events necessary to explain remaining discordances to obtain a fully connected ARG. While heuristic, our ARG reconstruction approach is often as accurate as more exact methods while being much more computationally efficient. Moreover, important demographic parameters such as recombination rates can be accurately estimated from reconstructed ARGs. Finally, we apply our approach to plant infecting RNA viruses in the genusPotyvirusto demonstrate how true recombination events can be disentangled from phylogenetic noise using our ARG reconstruction methods.
Xeno-free induced pluripotent stem cell-derived neural progenitor cells for in vivo applications
Authors: Rust Ruslan , Weber Rebecca Z. , Generali Melanie , Kehl Debora , Bodenmann Chantal , Uhr Daniela , Wanner Debora , Zürcher Kathrin J. , Saito Hirohide , Hoerstrup Simon P. , Nitsch Roger M. , Tackenberg Christian
Published: January 2022

Cell-based therapies are a promising treatment paradigm for neurodegenerative diseases and other brain injuries. Despite recent advances in stem cell technology, major concerns have been raised regarding the feasibility and safety of cell therapies for clinical applications. Here, we generate good manufacturing practice (GMP)-compatible neural progenitor cells (NPCs) from transgene- and xeno-free induced pluripotent stem cells (iPSCs) that can be smoothly adapted for clinical applications. The produced NPCs have a stable gene-expression over at least 15 passages and can be scaled for up to 1018 cells per initially seeded 106 cells. To ensure a pure NPC population for in vivo applications, we reduce risks of iPSC contamination using micro RNA-switch technology as a safety checkpoint. Using lentiviral transduction with a fluorescent and bioluminescent dual-reporter construct, combined with non-invasive in vivo bioluminescent imaging, we longitudinally tracked the grafted cells in healthy wild-type and genetically immunosuppressed mice as well as in a mouse model of ischemic stroke. Long term in-depth characterization revealed that transplanted cells have the capability to survive and spontaneously differentiate into functional and mature neurons throughout a time course of a month.
Connecting the dots: Harnessing dual-site transcranial magnetic stimulation to assess the causal influence of medial frontal areas on the motor cortex
Authors: Neige Cécilia , Vassiliadis Pierre , Zazou Abdelkrim Ali , Dricot Laurence , Lebon Florent , Brees Thomas , Derosiere Gerard
Published: January 2022

Dual-site transcranial magnetic stimulation (TMS) has been widely employed to investigate the influence of cortical structures on the primary motor cortex (M1). Here, we leveraged this technique to probe the causal influence of two key areas of the medial frontal cortex, namely the supplementary motor area (SMA) and the medial orbitofrontal cortex (mOFC), on M1. We show that SMA stimulation facilitates M1 activity across short (6 and 8 ms) and long (12 ms) inter-stimulation intervals, putatively recruiting cortico-cortical and cortico-subcortico-cortical circuits, respectively. Crucially, magnetic resonance imaging revealed that this facilitatory effect depended on a key morphometric feature of SMA: individuals with larger SMA volumes exhibited more facilitation from SMA to M1. Notably, we also provide evidence that the facilitatory effect of SMA stimulation at short intervals did not arise from spinal interactions of volleys descending simultaneously from SMA and M1. On the other hand, mOFC stimulation moderately suppressed M1 activity at both short and long intervals, irrespective of mOFC volume. These results suggest that dual-site TMS is an interesting tool to study the differential influence of SMA and mOFC on M1 activity, paving the way for the multi-modal assessment of these fronto-motor circuits in health and disease.

Key points

Dual-site TMS has been widely employed to investigate effective connectivity between cortical structures and the primary motor cortex (M1).

Here, we probed the causal influence of the supplementary motor area (SMA) and the medial orbitofrontal cortex (mOFC) on M1 activity.

SMA stimulation facilitates M1 activity at both short and long inter-stimulation intervals; this facilitatory effect is related to SMA volume.

mOFC stimulation moderately suppresses M1 activity, independent of mOFC volume.

The findings pave the way for multi-modal assessment of fronto-motor circuits in health and disease.
Merkel cell polyomavirus regulates miR183 cluster and piR62011 in Merkel cell carcinoma
Authors: Arora Reety , Dohadwala Lamiya , Nanavati Bageshri Naimish , Lakshmanan Vairavan , Mukherjee Sanjukta
Published: January 2022

Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer, a major subset of which is caused by the clonal integration of Merkel Cell Polyomavirus (MCV). Recent studies by Cheng et al. (2017) reported that virus-derived small T antigen protein-bound EP400 complex drives expression of genes essential for cellular transformation. On close analysis of their ChIP-Seq data, we uncovered that the complex binds to the promoter region of the microRNA-183 cluster. The miRNA183 cluster is a cluster of 3 miRNAs (miR183, 182 & 96) expressed and regulated together. These miRNAs are conserved across species, highly expressed in human embryonic stem cells and necessary for sensory/ mechanosensory organ development. We hypothesized that the MCV oncoproteins regulate host miRNA expression directly; an interaction novel in polyomaviruses. We tested miRNA expression via qPCR in both virus positive and negative MCC cell lines and found the former showed a much higher level. Further, fibroblasts expressing T antigens displayed an increase in miR182 expression in comparison to control. Knock-down of T antigens in MCC cells correspondingly decreased miR182 levels. To investigate its regulation we performed luciferase assays for the miRNA predicted promoter that showed increased activity in the presence of T antigens. Intriguingly, the seed sequence of miR182 completely matches to a piRNA called piR62011. Upon reanalysis of a MCC small RNA library, piR62011 emerged as the highest expressed. We found it expressed in MKL-1, a MCV positive cell line as well. Finally, to translate our findings into therapy for MCC, we screened small molecule (CMBL) library by performing surface plasmon resonance (SPR) assay and identified small molecules that binds to pre-miRNA182 and are testing them for their activity to kill MCC.
SARS-CoV-2 infection results in lasting and systemic perturbations post recovery
Authors: Frere Justin J. , Serafini Randal A. , Pryce Kerri D. , Zazhytska Marianna , Oishi Kohei , Golynker Ilona , Panis Maryline , Zimering Jeffrey , Horiuchi Shu , Hoagland Daisy A. , Møller Rasmus , Ruiz Anne , Overdevest Jonathan B. , Kodra Albana , Canoll Peter D. , Goldman James E. , Borczuk Alain C. , Chandar Vasuretha , Bram Yaron , Schwartz Robert , Lomvardas Stavros , Zachariou Venetia , tenOever Benjamin R.
Published: January 2022

SARS-CoV-2 has been found capable of inducing prolonged pathologies collectively referred to as Long-COVID. To better understand this biology, we compared the short- and long-term systemic responses in the golden hamster following either SARS-CoV-2 or influenza A virus (IAV) infection. While SARS-CoV-2 exceeded IAV in its capacity to cause injury to the lung and kidney, the most significant changes were observed in the olfactory bulb (OB) and olfactory epithelium (OE) where inflammation was visible beyond one month post SARS-CoV-2 infection. Despite a lack of detectable virus, OB/OE demonstrated microglial and T cell activation, proinflammatory cytokine production, and interferon responses that correlated with behavioral changes. These findings could be corroborated through sequencing of individuals who recovered from COVID-19, as sustained inflammation in OB/OE tissue remained evident months beyond disease resolution. These data highlight a molecular mechanism for persistent COVID-19 symptomology and characterize a small animal model to develop future therapeutics.
Broad-host-range mutagenesis with CRISPR-associated transposase
Authors: Rodríguez Lidimarie Trujillo , Ellington Adam J. , Reisch Christopher R.
Published: January 2022

Transposons have been instrumental tools in microbiology enabling random mutagenesis, with transposons like Tn5 and Mariner, and site-specific DNA integrations with Tn7. However, programmable targeting of transposons was impossible until CRISPR-associated transposase (CasTn) systems were described. Like other CRISPR-derived systems, CasTn can be programmed with a short DNA encoded sequence that is transcribed into a guide-RNA. Here we describe a broad-host-range CasTn system and demonstrate its function in bacteria from three classes of the Proteobacteria. The CasTn genes are expressed from a broad-host-range replicative plasmid, while the guide-RNA and transposon are provided on a high-copy pUC plasmid that is suicidal in most bacteria outside of E. coli. Using our CasTn system, single-gene disruptions were performed with on-target efficiencies approaching 100% in the Beta- and Gammaproteobacteria, Burkholderia thailandensis, and Pseudomonas putida, respectively. The results were more modest in the Alphaproteobacterium Agrobacterium fabrum, with a peak efficiency of 45%, though for routine single-gene disruptions, this efficiency is adequate. In B. thailandensis, the system allowed simultaneous co-integration of transposons at two different target sites. The CasTn system is also capable of high-efficiency large transposon insertion totaling over 11 kbp in P. putida. Given the iterative capabilities and large payload size, this system will be helpful for genome engineering experiments across several fields of research.

Significance

The genetic modification of bacteria to disrupt native genes and integrate recombinant genes is necessary for basic and applied research. Traditional methods for targeted disruptions and insertions are often cumbersome and inefficient, limiting experiments' scale and throughput. This work developed a system for targeted transposon mutagenesis that is easy to use, iterative, and efficient. We demonstrate that the system functions across three different classes of the Proteobacteria in species widely used in research and biotechnology. Moreover, the framework of the system and accompanying plasmids that we developed will facilitate porting the system to other bacteria. Our system provides a fast and efficient protocol to genetically modify these bacteria by inserting desired genetic cargo into specific genomic targets.
Matrix viscoelasticity controls spatio-temporal tissue organization
Authors: Elosegui-Artola Alberto , Gupta Anupam , Najibi Alexander J. , Seo Bo Ri , Garry Ryan , Darnell Max , Gu Wei , Zhou Qiao , Weitz David A. , Mahadevan L. , Mooney David J.
Published: January 2022

The spatio-temporal patterning of multicellular tissues is driven by the collective dynamics of cell proliferation and active movement. These processes are mediated by the extracellular matrix environment via a combination of biomolecular and physical cues. Here we show that the passive viscoelastic properties of the matrix that encapsulate a proliferating ball of cells (e.g. a developing organoid) play a critical role in guiding tissue organization in space and time. By varying the viscoelasticity of well-defined model matrices, we show how a spheroidal tissue of breast epithelial cells breaks symmetry and forms finger-like protrusions that invade the matrix. A computational model allows us to recapitulate these observations and leads to a phase diagram that demarcates the regions of morphological stability and instability as a function of matrix viscoelasticity, tissue viscosity, cell motility and cell division rate. Experiments that use biomolecular manipulations to independently vary these parameters confirm our predictions. To further test our theory, we also study the self-organization of an in-vitro intestinal organoid and show that the morphological changes of this system also fits within our paradigm. Altogether, our studies demonstrate the role of stress relaxation mechanisms in determining the dynamics of tissue growth and the symmetry breaking instabilities associated with branching, a fundamental process in morphogenesis and oncogenesis, and suggest ways of controlling tissue form using the extracellular matrix.
Lamin A/C phosphorylation at serine 22 is a conserved heat shock response to regulate nuclear adaptation during stress
Authors: Virtanen Laura , Holm Emilia , Halme Mona , West Gun , Lindholm Fanny , Gullmets Josef , Irjala Juho , Heliö Tiina , Padzik Artur , Meinander Annika , Eriksson John E. , Taimen Pekka
Published: January 2022

The heat shock (HS) response is crucial for cell survival in harmful environments. Nuclear lamin A/C, encoded by LMNA gene, has been shown to contribute towards altered gene expression during heat shock, but the underlying mechanisms are poorly understood. Here we show that reversible lamin A/C phosphorylation at Ser22 upon HS is an evolutionary conserved stress response that is triggered in concert with HSF1 activation in human and mouse cells and can also be observed in D. melanogaster in vivo. Consequently, the phosphorylation increase facilitated nucleoplasmic localization of lamin A/C and nuclear rounding in response to HS. The importance of lamin phosphorylation equilibria in HS was confirmed by lamin A/C knock-out (KO) cells that showed deformed nuclei after HS and were rescued by ectopic expression of wild-type, but not by a phosphomimetic (S22D) lamin A mutant. Furthermore, HS triggered release of lamina-associated protein 2α (Lap2α) from its association with lamin A/C and concurrently its downregulation, a response that was perturbed in lamin A/C KO cells and in LMNA mutant patient fibroblasts. The abrogated Lap2α response resulted in impaired cell cycle arrest under HS and compromised survival at the recovery. Taken together, our results suggest that the altered phosphorylation stoichiometry of lamin A/C provides an evolutionary conserved mechanism to regulate lamin structure and serve nuclear adaptation and cell survival during HS.
Macroscopic control of synchronous electrical signaling with chemically-excited gene expression
Authors: García-Navarrete M. , Avdovic Merisa , Pérez García S. , Ruiz Sanchis D. , Wabnik K.
Published: January 2022

Excitable cells can convert electrical signals into chemical outputs to facilitate the active transport of information across larger distances. This electrical-to-chemical conversion requires a tightly regulated expression of ion channels. Alterations of ion channel expression provide landmarks of numerous pathological diseases, such as cardiac arrhythmia, epilepsy, or cancer. Although the activity of ion channels can be locally regulated by external light or chemical stimulus, it remains challenging to coordinate the expression of ion channels on extended spatial-temporal scales in a non-invasive manner. Here, we have engineered yeast S. cerevisiae to read and convert local chemical concentrations into a dynamic electrical field distributed across cell populations. The core mechanism encodes a chemically-excitable dual-feedback gene circuit that precisely tunes the expression domain of potassium channels, globally coordinating cyclic firing of the plasma membrane potential (PMP). We demonstrate that this mechanism leverages an engineered constitutively open bacterial potassium channel KcsA to directly couple chemical stimuli with ion flux through gene expression and it can interface with the host ion channels through the pulsatile production of toxins. Our study provides a robust synthetic transcriptional toolbox underlying the conversion of local chemical environments into spatiotemporally organized electrical impulses for various cellular engineering, synthetic biology, and potential therapeutic applications.
Structural features of Dnase1L3 responsible for serum antigen clearance
Authors: McCord Jon J. , Engavale Minal , Masoumzadeh Elahe , Villarreal Johanna , Mapp Britney , Latham Michael P. , Keyel Peter A. , Sutton R. Bryan
Published: January 2022

Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 does not rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are several key differences between the two enzymes. Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. The CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA to prevent autoimmune pathology. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
Linking Dynamic DNA Secondary Structures to Genome Instability
Authors: Matos-Rodrigues Gabriel , van Wietmarschen Niek , Wu Wei , Tripathi Veenu , Koussa Natasha , Pavani Raphael , Nathan William , Belinky Frida , Mohammed Ashraf , Napierala Marek , Usdin Karen , Ansari Aseem Z. , Mirkin Sergei M. , Nussenzweig André
Published: January 2022

Genomic double-stranded DNA (dsDNA) becomes single-stranded (ssDNA) during replication, transcription, and DNA repair. ssDNA is therefore believed to be transient, occurring in only a fraction of the genome at a given time, and variable amongst a population of cells. These transiently formed ssDNA segments can also adopt alternative, dynamic DNA conformations, such as cruciform DNA, triplexes, quadruplexes and others. To determine whether there are stable and conserved regions of ssDNA, we utilized our previously developed method S1-END-seq 1 to convert ssDNA to DNA double strand breaks (DSBs), which are then processed for high-throughput sequencing. This approach revealed two predominant dynamic DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulated uniquely in microsatellite unstable human cancer cell lines, and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine (hPu/hPy) mirror repeats common across a variety of human cell lines. Triplex-forming repeats accumulated during replication, blocked DNA synthesis and were hotspots of somatic mutation. In contrast, pathologically expanded (hPu/hPy) repeats in Friedreich’s ataxia patient cells formed a replication-independent and transcription-inducible DNA secondary structure. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability.
The molecular and crystal structures of 2-(3-hydroxypropyl)benzimidazole and its nitrate salt
Authors: Rakhmonova Dilnoza , Kadirova Zukhra , Torambetov Batirbay , Kadirova Shakhnoza , Ashurov Jamshid , Shishkina Svitlana
Published: January 2022

2-(3-Hydroxypropyl)-1H-benzimidazole, C10H12N2O, which has potential biological activity, can be used as a ligand for complexation with metals. This compound is an electron donor, due to the lone pair of the nitrogen atom in the imidazole ring. This nitrogen atom also acts as a proton acceptor. In the crystalline phase, the nitrate salt, namely, 2-(3-hydroxypropyl)-1H-benzimidazol-3-ium nitrate, C10H13N2O+·NO3
−, has been studied. The protonation of the 2-(3-hydroxypropyl)benzimidazole unit results in significant delocalization of the electron density within the imidazole ring. The salt formation leads to variations in the intermolecular interactions, which were studied by analysis of the Hirshfeld surfaces and two-dimensional fingerprint plots.
Sustainability performance disclosures: the impact of gender diversity and intellectual capital on GRI standards compliance in Uganda
Authors: Bananuka Juma , Nkundabanyanga Stephen Korutaro , Kaawaase Twaha Kigongo , Mindra Rachel Katoroogo , Kayongo Isaac Newton
Published: January 2022

Purpose

The purpose of this study is to examine the extent of and impact of gender diversity and intellectual capital on compliance with Global Reporting Initiative (GRI) sustainability reporting standards by Uganda manufacturing companies.

Design/methodology/approach

Data were collected from manufacturing firms in Uganda using a questionnaire survey to find out their perception of compliance with the GRI standards. Data were analyzed using statistical package for social sciences, Microsoft Excel and smart partial least squares structural equation modeling (PLS–SEM).

Findings

The results indicate that on average, manufacturing firms in Uganda comply with GRI sustainability reporting standards to the extent of 59%. The results further indicate that manufacturing companies comply more with the GRI 200 (economic performance disclosures) to the extent of 63% as compared with 55% for GRI 300 (environmental performance disclosures) and 58% for GRI 400 (social performance disclosures). The results also indicate that intellectual capital has a significant impact on the GRI-based sustainability performance disclosures in Uganda. However, board gender diversity has no significant effect. In terms of the control variables, only firm size is significant, while firm age, capital structure and auditor type are not.

Originality/value

This study provides first time evidence of the extent of compliance with the GRI sustainability reporting standards using evidence from Uganda – an African developing country. This study widens the understanding of the usage of GRI standards in the preparation of sustainability reports by manufacturing firms in an emerging economy. This study also provides first-time evidence on the role of gender diversity and intellectual capital in GRI-based sustainability performance disclosures using evidence from Uganda's manufacturing sector.
Ancient routes, new gateways: a systematic literature review of China's cultural route heritage
Authors: Zhang Ke , González del Valle-Brena Almudena , Ramos Riera Ignacio , Zhao Jingli
Published: January 2022

Purpose

The study aims to understand how cultural route heritage is conceptualized and managed in China by systematically reviewing the research literature on Chinese cultural route heritage (CRH). The study intends to inspire further discussion on the theoretical and practical development of cultural routes since the development is still at a liminal stage in China.

Design/methodology/approach

A total of 253 research articles related to Chinese cultural rote heritage from major Chinese and English research databases China National Knowledge Infrastructure (CNKI), Web of Science (WOS) and Scopus have been comprehensively identified and reviewed for the purpose of the study.

Findings

Four major themes of research on Chinese CRH have been identified: conceptual evaluation, list of the routes and characteristics of the routes, conservation and utilization. The results revealed that China has very rich resources in CRH, many of which were formed a long time ago, which exist across vast geographic regions and have assumed multiple functions and undergone dynamic reciprocal exchanges among diverse cultures and ethnicities.

Practical implications

The paper summarizes some major obstacles faced by CRH in China and proposes a strategic model to address the need for a more sustainable development of CRH in the Chinese context.

Originality/value

The paper offers a comprehensive overview of CRH in China and discusses practical issues in management and development of heritage great in size, number and complexity.