bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads
Authors: Homberger Christina , Hayward Regan J , Barquist Lars , Vogel Jörg
Published: November 2022

Bulk RNA-sequencing technologies have provided invaluable insights into host and bacterial gene expression and associated regulatory networks. Nevertheless, the majority of these approaches report average expression across cell populations, hiding the true underlying expression patterns that are often heterogeneous in nature. Due to technical advances, single-cell transcriptomics in bacteria has recently become reality, allowing exploration of these heterogeneous populations, which are often the result of environmental changes and stressors. In this work, we have improved our previously published bacterial single-cell RNA-sequencing protocol that is based on MATQ-seq, achieving a higher throughput through the integration of automation. We also selected a more efficient reverse transcriptase, which led to reduced cell loss and higher workflow robustness. Moreover, we successfully implemented a Cas9-based ribosomal RNA depletion protocol into the MATQ-seq workflow. Applying our improved protocol on a large set of singleSalmonellacells sampled over growth revealed improved gene coverage and a higher gene detection limit compared to our original protocol and allowed us to detect the expression of small regulatory RNAs, such as GcvB or CsrB at a single-cell level. In addition, we confirmed previously described phenotypic heterogeneity inSalmonellain regards to expression of pathogenicity-associated genes. Overall, the low percentage of cell loss and high gene detection limit makes the improved MATQ-seq protocol particularly well suited for studies with limited input material, such as analysis of small bacterial populations in host niches or intracellular bacteria.

IMPORTANCE

Gene expression heterogeneity among isogenic bacteria is linked to clinically-relevant scenarios, like biofilm formation and antibiotic tolerance. The recent development of bacterial single-cell RNA-sequencing (scRNA-seq) enables the study of cell-to-cell variability in bacterial populations and the mechanisms underlying these phenomena. Here, we report a scRNA-seq workflow based on MATQ-seq with increased robustness, reduced cell loss, improved transcript capture rate, and gene coverage. Use of a more efficient reverse transcriptase and the integration of a ribosomal RNA depletion step, which can be adapted to other bacterial single-cell workflows, was instrumental for these improvements. Applying the protocol to the foodborne-pathogenSalmonella, we confirmed transcriptional heterogeneity across and within different growth phases and demonstrated that our workflow captures small regulatory RNAs on the single-cell level. Due to low cell loss and high transcript capture rates, this protocol is uniquely suited for experimental settings in which the starting material is limited, such as infected tissues.
A conserved complex of microneme proteins mediates rhoptry discharge inToxoplasma
Authors: Sidik Saima M. , Valleau Dylan , Acevedo-Sánchez Yamilex , Godoy Luiz C. , Pasaje Charisse Flerida A. , Huynh My-Hang , Carruthers Vern B. , Niles Jacquin C. , Lourido Sebastian
Published: November 2022

Apicomplexan parasites discharge specialized organelles called rhoptries upon host cell contact to mediate invasion. The events that drive rhoptry discharge are poorly understood, yet essential to sustain the apicomplexan parasitic life cycle. Rhoptry discharge appears to depend on proteins secreted from another set of organelles called micronemes, which inToxoplasma gondiiincludes MIC8 and the microneme-associated CRMP complex. Here, we examine the function of the microneme protein CLAMP, uncovering its essential role in rhoptry discharge. CLAMP forms a distinct complex with two other microneme proteins, the invasion-associated SPATR, and a previously uncharacterized protein we name CLAMP-linked invasion protein (CLIP). CLAMP-deficiency does not impact parasite adhesion or microneme protein secretion; however, knockdown of any member of the CLAMP complex affects rhoptry discharge. Phylogenetic analysis suggests orthologs of the essential complex components, CLAMP and CLIP, are ubiquitous across apicomplexans. Nevertheless, SPATR, which appears to act as an accessory factor inToxoplasma, is essential duringPlasmodium falciparumblood stages. Our results reveal a new protein complex that mediates rhoptry discharge following host-cell contact.
Theory on the rate equations of Michaelis-Menten type enzyme kinetics with competitive inhibition
Authors: Murugan R.
Published: November 2022

We derive approximate expressions under various conditions of validity over both pre- and post-steady state regimes of the velocity-substrate-inhibitor spaces of the Michaelis-Menten enzyme kinetic schemes with fully and partial competitive inhibition. Our refinement over the currently available standard quasi steady state approximations (sQSSA) seems to be valid over wide range of enzyme to substrate and enzyme to inhibitor ratios. Further, we show that under certain conditions the enzyme-inhibitor-substrate system can exhibit temporally well-separated two different steady states with respect to both enzyme-substrate and enzyme-inhibitor complexes. We define the ratiosfS=vmax⁄(KMS+e0) andfI=umax⁄(KMI+e0) as the acceleration factors with respect to the catalytic conversion of substrate and inhibitor into their respective products. HereKMSandKMIare the Michaelis-Menten parameters associated with the binding of substrate and inhibitor with the enzyme,vmaxandumaxare the respective maximum reaction velocities and e0, s0, and i0are total enzyme, substrate and inhibitor levels. When (fS⁄fI) < 1, then enzyme-substrate complex will show multiple steady states subsequently reaches the full-fledged steady state only after the depletion of enzyme-inhibitor complex. When (fS⁄fI) > 1, then the enzyme-inhibitor complex will show multiple steady states and subsequently reaches the full-fledged steady state only after the depletion of enzyme-substrate complex. This complex behavior exclusively when (fS⁄fI) ≠ 1 is the root cause of large amount of error in the estimation of various kinetic parameters both in the cases of fully and partial competitive inhibition schemes using the sQSSA methods. Remarkably, we show that our refined expressions for the reaction velocities over enzyme-substrate-inhibitor space can control this error more significantly than the currently available sQSSA velocity expressions.
An updated genome-scale model forXylella fastidiosasubsp.paucaDe Donno
Authors: Oliveira Alexandre , Cunha Emanuel , Silva Miguel , Faria Cristiana , Dias Oscar
Published: November 2022

Xylella fastidiosais a gram-negative phytopathogenic bacterium that caused a significant economic impact around the world. In the last decade, genome-scale metabolic models have become important systems biology tools for studying the metabolic behaviour of different pathogens and driving the discovery of novel drug targets. This work is a second iteration of the iMS508 model forX. fastidiosasubsp.paucaDe Donno. The model comprises 1138 reactions, 1234 metabolites, and 509 genes.in silicovalidation of the metabolic model was achieved through the comparison of simulations with available experimental data. Aerobic metabolism was simulated properly and fastidian gum production rates predicted accurately.
A dark matter insakebrewing: Origin of microbes producing aKimoto-style fermentation starter
Authors: Ito Kohei , Niwa Ryo , Kobayashi Ken , Nakagawa Tomoyuki , Hoshino Genki , Tsuchida Yuji
Published: November 2022

InKimoto-style fermentation, a fermentation starter is produced before the primary brewing process to stabilize fermentation. Nitrate-reducing bacteria, mainly derived from brewing water, produce nitrite, and lactic acid bacteria such asLeuconostoccan proliferate because of their tolerance towards low temperature and their low nutritional requirements. Later,Lactobacillusbecomes the dominant genus, leading to weakly acidic conditions that contribute to control yeasts and undesired bacterial contaminants. However, the sources of these microorganisms that play a pivotal role inSakebrewing have not yet been revealed. Thus, comprehensive elucidation of the microbiome is necessary. In this study, we performed 16S rRNA amplicon sequencing analysis after sampling from floor, equipment surfaces, and raw materials for making fermentation starters, includingkoji, and water inTsuchida Sakebrewery, Gunma, Japan. Amplicon sequence variants (ASVs) between the external environments and the fermentation starter were compared, and it was verified that the microorganisms in the external environments, such as built environments, equipment surfaces, and raw materials in the sake brewery, were introduced into the fermentation starter. Furthermore, various adventitious microbes present in the fermentation starter of early days and from the external environments were detected in a nonnegligible proportion in the starter, which may impact the taste and flavor. These findings illuminate the uncharacterized microbial dark matter of sake brewing, the sources of microbes inKimoto-style fermentation.
The human-specific miR-6762-5p is an activator of RhoA GTPase enhancingShigella flexneriintercellular spreading
Authors: Reisacher Caroline , Saifi Estelle , Ageron-Ardila Elisabeth , Mallmann Robert Theodor , Klugbauer Norbert , Skurnik David , Arbibe Laurence
Published: November 2022

MicroRNAs have recently emerged as major players in host-bacterial pathogens interaction, either as part of the host defense mechanism to neutralize infection or as a bacterial arsenal aimed at subverting host cell functions. Here we identify the newly evolutionary emerged human microRNA miR-6762-5p as a new player in the host-Shigellainterplay. A microarray analysis in infected epithelial cells allowed the detection of this miRNA exclusively during the late phase of infection. Conditional expression of miR-6762-5p combined with a transcriptome analysis indicated a role in cytoskeleton remodeling. Likewise, miR-6762-5p enhanced stress fibers formation through RhoA activation andin silicoanalysis identified several regulators of RhoA activity as potential direct transcriptional targets. We further showed that miR-6762-5p expression induces an increase inShigellaintercellular spreading, while miR-6762-5p inhibition reduced bacterial dissemination. Overall, we have identified a human-specific miR-6762-5p acting specifically at theShigelladissemination step. We propose a model in which the expression of miR-6762-5p induces cytoskeleton modifications through RhoA activation to achieve a successful dissemination ofShigellain the host.
Remembering the “When”: Hebbian Memory Models for the Time of Past Events
Authors: Brea Johanni , Modirshanechi Alireza , Iatropoulos Georgios , Gerstner Wulfram
Published: November 2022

Humans and animals can remember how long ago specific events happened. In contrast to interval-timing on the order of seconds and minutes, little is known about the neural mechanisms that enable remembering the “when” of autobiographical memories stored in the episodic memory system. Based on a systematic exploration of neural coding, association and retrieval schemes, we develop a family of hypotheses about the reconstruction of the time of past events, consistent with Hebbian plasticity in neural networks. We compare several plausible candidate mechanism in simulated experiments and, propose how combined behavioral and physiological experiments can be used to pin down the actual neural implementation of the memory for the time of past events.
Acquisition, co-option, and duplication of thertxtoxin system and the emergence of virulence inKingella
Authors: Morreale Daniel P. , Porsch Eric A. , Kern Brad K. , Geme Joseph W. St , Planet Paul J.
Published: November 2022

TheKingellagenus includes two pathogenic species, namelyK. kingaeandK. negevensis, as well as strictly commensal species. BothK. kingaeandK. negevensissecrete a toxin called RtxA that is absent in the commensal species. Phylogenetic analysis demonstrates that the toxin-encoding operonrtxCrtxAtolCwas acquired by a common ancestor of the pathogenicKingellaspecies and that a preexisting type I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% ofK. kingaestrains containing two copies of thertxAtoxin gene. ThertxAduplication is largely clonal and strongly associated with invasive disease. In assays with isogenic strains, a single copy ofrtxAwas associated with reduced virulencein vitro. This study establishes the critical steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.
Glucose modulates transcription factor dimerization to enable tissue differentiation
Authors: Lopez-Pajares Vanessa , Bhaduri Aparna , Zhao Yang , Gowrishankar Gayatri , Donohue Laura , Guo Margaret G. , Siprashvili Zurab , Miao Weili , Nguyen Duy T. , Li Albert M. , Shanderson Ronald L. , Meyers Robin M. , Guerrero Angela , Ji Andrew L. , Garcia Omar S. , Tao Shiying , Meservey Lindsey M. , Yang Xue , Gambhir Sanjiv S. , Ye Jiangbin , Khavari Paul A.
Published: November 2022

Glucose is a universal energy currency for living organisms, however, its non-energetic functions in processes such as differentiation are undefined. In epidermis, differentiating cells exhibit dynamic changes in gene expression1–4driven by specific transcription factors (TFs)5–9. The interplay between such TFs and biomolecules that also change in this process is not understood. Metabolomic analyses revealed that increased intracellular glucose accompanies differentiation of epidermal keratinocytes. This elevation also occurred in differentiating cells from other tissues and was verified in epidermal tissue engineered with glucose sensors, which detected a glucose gradient that peaked in the outermost differentiated layers. Free glucose accumulation, unaccompanied by its increased metabolism, was essential for epidermal differentiation and required GLUT1, GLUT3, and SGLT1 transporters. Glucose affinity chromatography and azido-glucose click chemistry uncovered glucose binding to diverse regulatory proteins, including the IRF6 TF, whose epidermal knockout confirmed its requirement in glucose-dependent differentiation. Direct glucose binding enabled IRF6 dimerization, DNA binding, genomic localization, and induction of IRF6 target genes, including essential pro-differentiation TFsGRHL1, GRHL3, HOPXandPRDM1. The IRF6R84Cmutant found in undifferentiated cancers was unable to bind glucose. These data identify a new role for glucose as a gradient morphogen that modulates protein multimerization in cellular differentiation.
Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers
Authors: Singh Anurag Kumar , Walavalkar Kaivalya , Tavernari Daniele , Ciriello Giovanni , Notani Dimple , Sabarinathan Radhakrishnan
Published: November 2022

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often the HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes (such as E6/E7) is well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. Here, we investigate the genome-wide patterns of HPV integrations and associated host gene expression changes in the context of chromatin states and topologically associating domains (TADs). We find that HPV integrations are significantly enriched and depleted in active and inactive chromatin regions, respectively. Interestingly, regardless of the chromatin state, the genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, the upregulation (both local and long-range) is mostly confined to the TADs with integration and does not affect the adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (such asMYC, PVT1, TP63andERBB2), regardless of the proximity. To further understand the long-range effect, we performed HiC and 4C-seq analyses in HeLa and observed chromatin looping interaction between the integrated HPV andMYC/PVT1regions (situated ∼500 kb apart), leading to allele-specific overexpression of these genes. Again, these chromatin interactions involving integrated HPV are mostly observed within the same TAD. Together, these results suggest the cis-regulatory potential of integrated HPV DNA that drives host gene upregulation at intra-TAD level in cervical cancer. Based on this, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.
Migration and the excess exposure of birds to human density in North America
Authors: Jackson Erin K. , Dakin Roslyn
Published: November 2022

Migratory species must cross a range of landscapes that are increasingly modified by humans. A key question is how migrating populations are responding to human-induced environmental change. Here, we model the spring migration dynamics of 63 bird species in North America to quantify their exposure to human population density. We find that most bird species have a negative navigational bias, suggesting that they attempt to avoid human-dense areas during migration, and yet they experience far greater human density during migration as compared to breeding. Species that experience excess human density during migration share several key traits: they tend to be nocturnal migrants, they start migrating through North America earlier in the year, and they tend to migrate longer distances. These findings underscore that birds are especially vulnerable to threats associated with human disturbance during migration, with predictable exposures that are often elevated by 2- to 3-fold during migration.
Attentional modulation is orthogonal to disinhibition by VIP interneurons in primary visual cortex
Authors: Myers-Joseph Dylan , Wilmes Katharina A. , Fernandez-Otero Marian , Clopath Claudia , Khan Adil G.
Published: November 2022

Attentional modulation of sensory processing is a key feature of cognition, yet its neural circuit basis is poorly understood. A candidate mechanism is the disinhibition of pyramidal cells through vasoactive intestinal peptide (VIP) and somatostatin (SOM) positive interneurons. However, the interaction of attentional modulation and VIP-SOM disinhibition has never been directly tested. We used all-optical methods to bi-directionally manipulate VIP interneuron activity as mice performed an attention switching task. We measured the activity of VIP, SOM and parvalbumin (PV) positive interneurons and pyramidal neurons identified in the same tissue and found that although activity in all cell classes was modulated by both attention and VIP manipulation, their effects were orthogonal. Attention and VIP-SOM disinhibition relied on distinct patterns of changes in activity and reorganisation of interactions between inhibitory and excitatory cells. Circuit modelling revealed a precise network architecture consistent with multiplexing strong yet non-interacting modulations in the same neural population.
Inferring Cognitive State Underlying Conflict Choices in Verbal Stroop Task Using Heterogeneous Input Discriminative-Generative Decoder Model
Authors: Rezaei Mohammad R. , Jeoung Haseul , Gharamani Ayda , Saha Utpal , Bhat Venkat , Popovic Milos R. , Yousefi Ali , Chen Robert , Lankarany Milad
Published: November 2022

The subthalamic nucleus (STN) of the basal ganglia interacts with the medial prefrontal cortex (mPFC) and shapes a control loop, specifically when the brain receives contradictory information from either different sensory systems or conflicting information from sensory inputs and prior knowledge that developed in the brain. Experimental studies demonstrated that significant increases in theta activities (2-8 Hz) in both the STN and mPFC as well as increased phase synchronization between mPFC and STN are prominent features of conflict processing. While these neural features reflect the importance of STN-mPFC circuitry in conflict processing, a low-dimensional representation of the mPFC-STN interaction referred to as a cognitive state, that links neural activities generated by these sub-regions to behavioral signals (e.g., the response time), remains to be identified. Here, we propose a new model, namely, the heterogeneous input discriminative-generative decoder (HI-DGD) model, to infer a cognitive state underlying decision-making based on neural activities (STN and mPFC) and behavioral signals (individuals’ response time) recorded in 10 Parkinson’s disease patients while they performed a Stroop task. PD patients may have conflict processing which is quantitatively (may be qualitative in some) different from healthy population. Using extensive synthetic and experimental data, we showed that the HI-DGD model can diffuse information from neural- and behavioral data simultaneously and estimate cognitive states underlying conflict and nonconflict trials significantly better than traditional methods. Additionally, the HI-DGD model identified which neural features made significant contributions to conflict and non-conflict choices. Interestingly, the estimated features match well with those reported in experimental studies. Finally, we highlight the capability of the HI-DGD model in estimating a cognitive state from a single trial of observation, which makes it appropriate to be utilized in closed-loop neuromodulation systems.

Highlights

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Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales
Authors: Herting Julian , Schönenberger Jürg , Sauquet Hervé
Published: November 2022

Premise of the Study

Recent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors.

Methods

Here, we compiled a dataset of 33 floral characters scored for 414 extant ericalean species sampled from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal rates Markov models for each trait. We used the rates estimated during the ancestral state reconstruction for comparing evolutionary rates between flower modules, creating a “rate profile” of ericalean flowers.

Key Results

The androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve slower. High and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral dataset reveal that this pattern appears to be conserved across most major angiosperm clades.

Conclusions

Elevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. We discuss the implications of heterogenous morphological rates of evolution among floral modules from a functional perspective. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.
Extensive somatic nuclear exchanges shape global populations of the wheat leaf rust pathogenPuccinia triticina
Authors: Sperschneider Jana , Hewitt Tim , Lewis David C. , Periyannan Sambasivam , Milgate Andrew W. , Hickey Lee T. , Mago Rohit , Dodds Peter N. , Figueroa Melania
Published: November 2022

Non-sexual processes such as somatic nuclear exchange are postulated to play a role in the diversity of clonally reproducing dikaryotic rust fungi but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies ofPuccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage is derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveal that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.
AATF Inhibition Exerts Antiangiogenic Effects Against Human Hepatocellular Carcinoma
Authors: Suresh Diwakar , Srinivas Akshatha N. , Prashant Akila , Satish Suchitha , Vishwanath Prashant , Santhekadur Prasanna K. , Kumar Divya P.
Published: November 2022

Hepatocellular carcinoma (HCC), a highly fatal cancer with a mortality rate proportional to its incidence, continues to pose a global health care challenge. Angiogenesis is a key factor in the growth and metastasis of hepatic tumors and thus a potential therapeutic target in HCC. We previously showed that the apoptosis antagonizing transcription factor (AATF) affects tumor growth and metastasis in a mouse xenograft model. However, the regulatory role of AATF in tumor angiogenesis and its underlying mechanisms in HCC remain unknown. In the current study, we identified high levels of AATF in human HCC tissues compared to adjacent normal liver tissues, and the expression was found to be correlated with the stages and tumor grades of HCC. Inhibition of AATF in human HCC cells showed high levels of pigment epithelium-derived factor (PEDF) compared to controls as a resultant of reduced matric metalloproteinases activity. Conditioned media from AATF knockdown (KD) cells inhibited the proliferation, migration, and invasion of human umbilical vein endothelial cells as well as the vascularization of the chick chorioallantoic membrane. Furthermore, the VEGF-mediated downstream signaling pathway responsible for endothelial cell survival and vascular permeability, cell proliferation, and migration favoring angiogenesis was suppressed by AATF inhibition. Of note, PEDF inhibition by its respective antibody profoundly reversed the anti-angiogenic effect of AATF KD. In conclusion, our study demonstrates that inhibition of AATF suppresses angiogenesis in HCC via PEDF. Thus, a therapeutic strategy based on the inhibition of AATF to disrupt tumor angiogenesis may be a promising approach for HCC treatment.
Review and further developments in statistical corrections for Winner’s Curse in genetic association studies
Authors: Forde Amanda , Hemani Gibran , Ferguson John
Published: November 2022

Genome-wide association studies (GWAS) are commonly used to identify genomic variants that are associated with complex traits, and estimate the magnitude of this association for each variant. However, it has been widely observed that the association estimates of variants tend to be lower in a replication study than in the study that discovered those associations. A phenomenon known asWinner’s Curseis responsible for this upward bias present in association estimates of significant variants in the discovery study. We review existingWinner’s Cursecorrection methods which require only GWAS summary statistics in order to make adjustments. In addition, we propose modifications to improve existing methods and propose a novel approach which uses the parametric bootstrap. We evaluate and compare methods, first using a wide variety of simulated data sets and then, using real data sets for three different traits. The metric, estimated mean squared error (MSE) over significant SNPs, was primarily used for method assessment. Our results indicate that widely used conditional likelihood based methods tend to perform poorly. The other considered methods behave much more similarly, with our proposed bootstrap method demonstrating very competitive performance. To complement this review, we have developed an R package, ‘winnerscurse’ which can be used to implement these variousWinner’s Curseadjustment methods to GWAS summary statistics.

Author Summary

A genome-wide association study is designed to analyse many common genetic variants in thousands of samples and identify which variants are associated with a trait of interest. It provides estimates of association strength for each variant and variants are classified as associated if their test statistics obtained in the study pass a chosen significance threshold. However, due to a phenomenon known asWinner’s Curse,the association estimates of these significant variants tend to be upward biased and greater in magnitude than their true values. Naturally, this bias has adverse consequences for downstream statistical techniques which use these estimates. In this paper, we look at current methods which have been designed to combatWinner’s Curseand propose modifications to these methods in order to improve performance. Using a wide variety of simulated data sets as well as real data, we perform a thorough evaluation of these methods. We use a metric which allows us to identify which methods, on average, produce adjusted estimates for significant variants that are closest to the true values. To accompany our work, we have created an R package, ‘winnerscurse’, which allows users to easily applyWinner’s Cursecorrection methods to their data sets.
Limited oxygen availability in standard cell culture alters metabolism and function in terminally-differentiated cells
Authors: Tan Joycelyn , Virtue Sam , Norris Dougall M. , Conway Olivia J. , Yang Ming , Gribben Christopher , Lugtu Fatima , Kamzolas Ioannis , Krycer James R. , Mills Richard J. , Pereira Conceição , Dale Martin , Shun-Shion Amber S. , Baird Harry J. M. , Horscroft James A. , Sowton Alice P. , Ma Marcella , Carobbio Stefania , Petsalaki Evangelia , Murray Andrew J. , Gershlick David C. , Hudson James E. , Vallier Ludovic , Fisher-Wellman Kelsey H , Frezza Christian , Vidal-Puig Antonio , Fazakerley Daniel J.
Published: November 2022

Cell culture is generally considered to be hyperoxic. However, the importance of cellular oxygen consumption is often underappreciated, with rates of oxygen consumption often sufficient to cause hypoxia at cell monolayers. We initially focused on cultured adipocytes as a terminally differentiated cell-type with substantial oxygen consumption rates to support diverse cellular functions. Under standard conditions, cultured adipocytes are hypoxic and highly glycolytic. Increasing oxygen diverted glucose flux toward mitochondria and resulted in thousands of gene expression changes that pointed toward alleviated physiological transcriptional responses to hypoxia. Phenotypically, providing more oxygen increased adipokine secretion and rendered adipocytes more sensitive to insulin and lipolytic stimuli. The functional benefits of increasing pericellular oxygen were transferable to other cellular systems including hPSC-derived hepatocytes and cardiac organoids. Our findings suggest that oxygen is limiting in many terminally-differentiated cell culture systems, and that controlling oxygen availability can improve the quality and translatability of cell models.
Utilization of anArtery-on-a-chipto unravel novel regulators and therapeutic targets in vascular diseases
Authors: Paloschi Valentina , Pauli Jessica , Winski Greg , Wu Zhiyuan , Li Zhaolong , Glukha Nadiya , Hummel Nora , Rogowitz Felix , Meucci Sandro , Botti Lorenzo , Busch Albert , Chernogubova Ekaterina , Jin Hong , Sachs Nadja , Eckstein Hans-Henning , Dueck Anne , Boon Reinier A. , Bausch Andreas R. , Maegdefessel Lars
Published: November 2022

Introduction

Organs-on-chips represent novelin vitromodels that have the capacity to emulate aspects of human physiology and pathophysiology by incorporating features like tissue-multicellularity and exposure to organ-relevant physical environment. We developed anartery-on-a-chipwith the objective to recapitulate the structure of the arterial wall composed of intimal and medial layers and the relevant hemodynamic forces that affect luminal cells.

Results

By comparingarteries-on-chipsexposed either toin vivo-like shear stress values or kept in static conditions, we identified a panel of novel genes modulated by shear stress. We next measured the expression pattern of shear stress-modulated genes in areas of the vascular tree affected by atherosclerotic plaques and aortic aneurysms, where disease development and progression are induced by alterations of shear stress. We obtained biopsies from patients affected by carotid artery disease (CAD), comprising the atherosclerotic plaque (diseased artery) and the adjacent region (non-diseased artery). From patients with abdominal aortic aneurysms (AAA), we obtained the aneurysmal portion (diseased aorta) and non-dilated adjacent segment (non-diseased aorta). Genes modulated by shear stress followed the same expression pattern in non-diseased segments of human vessels and were expressed by endothelial and smooth muscle cells as evidenced by immunofluorescence analysis and single cell RNA sequencing. Using mice and porcine models of vascular CAD and AAA, we confirmed that shear stress mediated targets are important in discriminating diseased and non-diseased vessel portionsin vivo. Furthermore, we showed that ourartery-on-a-chipcan serve as a platform for drug-testing. We were able to reproduce the effects of a therapeutic agent previously used in AAA animal models inartery-on-a-chipsystems and extend our understanding of its therapeutic effect through a multicellular structure.

Conclusions

Our novelin vitromodel is capable of mimicking important physiological aspects of human arteries, such as the response to shear stress, and can further shed light on the mechanism of action of potential therapeutics before they enter the clinical stage.

Teaser

Theartery-on-a-chipis a novelin vitroplatform that enables the mimicry of human arteries and can be used to gain insights into the development and therapeutic targeting of vascular diseases.
Structural and functional specializations of human fast spiking neurons support fast cortical signaling
Authors: Wilbers René , Galakhova Anna A. , Driessens Stan L.W. , Heistek Tim S. , Metodieva Verjinia D. , Hagemann Jim , Heyer Djai B. , Mertens Eline J. , Deng Suixin , Idema Sander , Witt Hamer Philip C. de , Noske David P. , van Schie Paul , Kommers Ivar , Luan Guoming , Li Tianfu , Shu Yousheng , de Kock Christiaan P.J. , Mansvelder Huibert D. , Goriounova Natalia A.
Published: November 2022

Fast spiking interneurons (FSINs) provide fast inhibition that synchronizes neuronal activity and is critical for cognitive function. Fast synchronization frequencies are evolutionary conserved in the expanded human neocortex, despite larger neuron-to-neuron distances that challenge fast input-output transfer functions of FSINs. Here, we test in human neurons from neurosurgery tissue which mechanistic specializations of human FSINs explain their fast-signaling properties in human cortex. With morphological reconstructions, multi-patch recordings, and biophysical modeling we find that despite three-fold longer dendritic path, human FSINs maintain fast inhibition between connected pyramidal neurons through several mechanisms: stronger synapse strength of excitatory inputs, larger dendrite diameter with reduced complexity, faster AP initiation, and faster and larger inhibitory output, while Na+current activation/inactivation properties are similar. These adaptations underlie short input-output delays in fast inhibition of human pyramidal neurons through FSINs, explaining how cortical synchronization frequencies are conserved despite expanded and sparse network topology of human cortex.

Teaser/one-sentence summary

Specializations of fast spiking human neurons ensure fast signaling in human cortex.
Characterisation of the functional and transcriptomic effects of pro-inflammatory cytokines on human EndoC-βH5 beta cells
Authors: Frørup Caroline , Gerwig Rebekka , Søndergaard Svane Cecilie Amalie , Mendes Lopes de Melo Joana , Fløyel Tina , Pociot Flemming , Kaur Simranjeet , Størling Joachim
Published: November 2022

Objective

EndoC-βH5 is a newly established human beta-cell model which may be superior to previous models of native human beta cells. Exposure of beta cells to proinflammatory cytokines is a widely used in vitro model of immune-mediated beta-cell failure in type 1 diabetes and we therefore performed an in-depth characterisation of the effects of cytokines on EndoC-βH5 cells.

Methods

The sensitivity profile of EndoC-βH5 cells to the toxic effects of the pro-inflammatory cytokines interleukin-1β (IL-1β), interferon γ (IFNγ) and tumour necrosis factor-α (TNFα) was examined in titration and time-course experiments. Cell death was evaluated by caspase 3/7 activity, cytotoxicity, viability, TUNEL assay and immunoblotting. Mitochondrial function was evaluated by extracellular flux technology. Activation of signalling pathways and major histocompatibility complex (MHC) class I expression were examined by immunoblotting, immunofluorescence, and real-time quantitative PCR (qPCR). Glucose-stimulated insulin secretion (GSIS) and cytokine-induced chemokine secretion were measured by ELISA and Meso Scale Discovery multiplexing electrochemiluminescence, respectively. Global gene expression was characterised by stranded RNA sequencing.

Results

Cytokines increased caspase activity and cytotoxicity in EndoC-βH5 cells in a time- and dose-dependent manner. The proapoptotic effect of cytokines was primarily driven by IFNγ. Cytokine exposure caused impaired mitochondrial function, diminished GSIS, and induced secretion of chemokines. At the signalling level, cytokines increased the phosphorylation of signal transducer and activator of transcription 1 (STAT1) but not c-jun N-terminal kinase (JNK) and did not cause degradation of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor α (IκBα). MHC class I was induced by cytokines. Cytokine exposure caused significant changes to the EndoC-βH5 transcriptome including upregulation ofHLAgenes, endoplasmic reticulum stress markers, and non-coding RNAs. Among the differentially expressed genes were several type 1 diabetes risk genes.

Conclusions

Our study provides detailed insight into the functional and transcriptomic effects of cytokines on EndoC-βH5 cells. This knowledge will be helpful for future investigations studying cytokine effects in this cell model.
Reward does not modulate forgetting in free recall tests
Authors: Hellerstedt Robin , Talmi Deborah
Published: November 2022

Reward is thought to attenuate forgetting through the automatic effect of dopamine on hippocampal memory traces. Here we report a conceptual replication of previous results where we did not observe this effect of reward. Participants encoded eight lists of pictures and recalled picture content immediately or the next day. They were informed that they could gain monetary reward for recalling the pictures, with the level of reward indicated through the frame surrounding the picture. Reward was manipulated both within and across lists. Bayesian statistics found moderate evidence for the null hypothesis that reward does not modulate forgetting in human free recall.
Magnetic, electric and toroidal polarization modes describing the physical properties of crystals. NdFeO3 case
Authors: Fabrykiewicz Piotr , Przeniosło Radosław , Sosnowska Izabela
Published: November 2022

The structure and the physical phenomena that occur in a crystal can be described by using a suitable set of symmetry-adapted modes. The classification of magnetic modes in crystals presented in Fabrykiewicz et al. [Acta Cryst. (2021), A77, 327–338] is extended to a classification of electric and toroidal (anapole) modes in crystals. These three classifications are based on magnetic point groups, which are used in two contexts: (i) the magnetic point group of the magnetic crystal class and (ii) the magnetic site-symmetry point group of the Wyckoff position of interest. The classifications for magnetic, electric and toroidal modes are based on the properties of the three generalized inversions: space inversion 1, time inversion 1′ and the space-and-time inversion 1′. It is emphasized that none of these three inversions is more important than the other two. A new notation for symmetry operation symbols and magnetic point group symbols is proposed; each operation is presented as a product of one proper rotation and one generalized inversion. For magnetic, electric and toroidal orderings there are 64 modes: three pure ferro(magnetic/electric/toroidal) modes, 13 mixed ferro(magnetic/electric/toroidal) and antiferro(magnetic/electric/toroidal) modes, and 48 pure antiferro(magnetic/electric/toroidal) modes. The proposed classification of modes leads to useful observations: the electric and toroidal modes have many symmetry limitations similar to those already known for the magnetic modes, e.g. a continuous reorientation of the magnetic or electric or toroidal moments is possible only in triclinic or monoclinic symmetry. An antiferro(magnetic/electric/toroidal) ordering with a weak perpendicular ferro(magnetic/electric/toroidal) component is possible only in monoclinic or orthorhombic symmetry. The general classifications of magnetic, electric and toroidal modes are presented for the case of NdFeO3.
The welding tracking technology of an underwater welding robot based on sliding mode active disturbance rejection control
Authors: Li Shengqian , Zhang Xiaofan
Published: November 2022

Purpose

A welding robot is a complicated system with uncertainty, time-varying, strong coupling and non-linear system. It is more complicated if it is used in an underwater environment. It is difficult to establish an accurate dynamic model for an underwater welding robot. Aiming at the tracking control of an underwater welding robot, it is difficult to achieve the control performance requirements by the classical proportional integral derivative control method to realize automatic tracking of the seam. The purpose of this paper is to suggest a novel method to deal with these issues.

Design/methodology/approach

To combine the advantages of active disturbance rejection control (ADRC) and sliding mode control (SMC) to improve the shortcomings of a single control method, a hybrid control method for an underwater welding robot trajectory tracking based on SMC_ADRC is proposed in this research work.

Findings

The simulation experiment of the proposed approach is carried out by Matlab/Simulink, and the welding experiment is recorded. The seam gets plumper and smoother, with better continuity and no undercut phenomenon.

Originality/value

The proposed approach is effective and reliable, and the system’s tracking performance is stable, which can effectively reduce chattering and improve system robustness.
Review Papers Examining accountability in relation to local football communities
Authors: Burns John Edward , Jollands Stephen
Published: November 2022

Purpose

Most football clubs were founded by members of the local community within which they are based. The success of a club is built on the time, effort and resources given by these locals, which is offered due to the benefits that football promises to the community in return. However, the game has increasingly been dominated by a focus on financial (monetary) value, at the expense of such benefits being delivered to the clubs' local communities. This article examines a need for deliberation over what accountability is owed by football clubs to their local communities in the context of questioning what and for whom football is for.

Design/methodology/approach

This exploration is undertaken within the context of the English game, where a series of issues has resulted in the UK Government undertaking a “fan led review of football governance”. The report produced by this review is analysed to understand whether the contents and recommendations enters the debate over what accountability is owed to local communities.

Findings

While the UK Government's fan led review recognises the pivotal role of local communities in the formation of the English game, its focus and resulting recommendations are mostly on the financial sustainability of the clubs. The analysis demonstrates that, due to their focus on financial value, the implementation of the report's recommendations is more likely to exacerbate the underlying issues rather than resolving them.

Originality/value

The call for deliberation over whether and what accountability is owed to local communities has been repeated over time. The UK Government's fan led review provided an important opportunity to engage in that deliberation. However, the dominance of financial value within football has all but silenced any call for and action regarding this.
Sustainability and technology: the contribution of “managerial talk” to the three pillars framework
Authors: Golubeva Olga
Published: November 2022

Purpose

This article investigates whether accounting, a tool that affects the actions of both organisations and society, can contribute to further developing the concept of sustainability. Exploiting real-time accounts of management speeches, termed “managerial talk” in the context of this paper, the study is among the first to include technology within a sustainability framework.

Design/methodology/approach

A data structure with first-order and second-order categories was created using a methodology elaborated by Van Maanen (1979) and Gioia et al. (2012). The empirical data was collected during 20 presentations delivered by senior managers from companies, the financial industry, the Swedish government and non-profit organisations to the Swedish Society of Financial Analysts between November 2016 and February 2020.

Findings

The study develops an inductive model that emerges as a result of the data analysis process. It emphasises that technology can be both an enabler for, and an interference with, sustainability according to the application of steering mechanisms. The latter include governance and regulations, analysis and evaluation tools, and disclosure practice.

Research limitations/implications

Acknowledging the role of technology in sustainable development can potentially assist in the implementation of sustainability and, arguably, in fostering an alignment between the three pillars of sustainability.

Originality/value

Interrelationships between sustainability, technology and accounting comprise a relatively unexplored research setting that has seldom been at the centre of academic studies.