bluuebunny/crossref_metadata_2025 huggingface dataset:
Ontogeny of collective behaviour
Authors: Muratore Isabella Benter , Garnier Simon
Published: February 2023

During their lifetime, superorganisms, like unitary organisms, undergo transformations that change the machinery of their collective behaviour. Here, we suggest that these transformations are largely understudied and propose that more systematic research into the ontogeny of collective behaviours is needed if we hope to better understand the link between proximate behavioural mechanisms and the development of collective adaptive functions. In particular, certain social insects engage in self-assemblage, forming dynamic and physically connected architectures with striking similarities to developing multicellular organisms, making them good model systems for ontogenetic studies of collective behaviour. However, exhaustive time series and three-dimensional data are required to thoroughly characterize the different life stages of the collective structures and the transitions between these stages. The well-established fields of embryology and developmental biology offer practical tools and theoretical frameworks that could speed up the acquisition of new knowledge about the formation, development, maturity and dissolution of social insect self-assemblages and, by extension, other superorganismal behaviours. We hope that this review will encourage an expansion of the ontogenetic perspective in the field of collective behaviour and, in particular, in self-assemblage research, which has far-reaching applications in robotics, computer science and regenerative medicine.

This article is part of a discussion meeting issue ‘Collective behaviour through time’.
Multispecies collective waving behaviour in fish
Authors: Lukas Juliane , Krause Jens , Träger Arabella Sophie , Piotrowski Jonas Marc , Romanczuk Pawel , Sprekeler Henning , Arias-Rodriguez Lenin , Krause Stefan , Schutz Christopher , Bierbach David
Published: February 2023

Collective behaviour is widely accepted to provide a variety of antipredator benefits. Acting collectively requires not only strong coordination among group members, but also the integration of among-individual phenotypic variation. Therefore, groups composed of more than one species offer a unique opportunity to look into the evolution of both mechanistic and functional aspects of collective behaviour. Here, we present data on mixed-species fish shoals that perform collective dives. These repeated dives produce water waves capable of delaying and/or reducing the success of piscivorous bird attacks. The large majority of the fish in these shoals consist of the sulphur molly,
Poecilia sulphuraria
, but we regularly also found a second species, the widemouth gambusia,
Gambusia eurystoma
, making these shoals mixed-species aggregations. In a set of laboratory experiments, we found that gambusia were much less inclined to dive after an attack as compared with mollies, which almost always dive, though mollies dived less deep when paired with gambusia that did not dive. By contrast, the behaviour of gambusia was not influenced by the presence of diving mollies. The dampening effect of less responsive gambusia on molly diving behaviour can have strong evolutionary consequences on the overall collective waving behaviour as we expect shoals with a high proportion of unresponsive gambusia to be less effective at producing repeated waves.

This article is part of a discussion meeting issue ‘Collective behaviour through time’.
Indirect genetic effects for social network structure in
Drosophila melanogaster
Authors: Wice Eric Wesley , Saltz Julia Barbara
Published: February 2023

The position an individual holds in a social network is dependent on both its direct and indirect social interactions. Because social network position is dependent on the actions and interactions of conspecifics, it is likely that the genotypic composition of individuals within a social group impacts individuals' network positions. However, we know very little about whether social network positions have a genetic basis, and even less about how the genotypic makeup of a social group impacts network positions and structure. With ample evidence indicating that network positions influence various fitness metrics, studying how direct and indirect genetic effects shape network positions is crucial for furthering our understanding of how the social environment can respond to selection and evolve. Using replicate genotypes of
Drosophila melanogaster
fruit flies, we created social groups that varied in their genotypic makeup. Social groups were videoed, and networks were generated using motion-tracking software. We found that both an individual's own genotype and the genotypes of conspecifics in its social group affect its position within a social network. These findings provide an early example of how indirect genetic effects and social network theory can be linked, and shed new light on how quantitative genetic variation shapes the structure of social groups.

This article is part of a discussion meeting issue ‘Collective behaviour through time’.
Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China
Authors: Jones Adrian , Zhang Daoyu , Massey Steven E. , Deigin Yuri , Nemzer Louis R. , Quay Steven C.
Published: February 2023

HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence,Tylonycteris pachypusbat isolate BtTp-GX2012. Usingin silicomodeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.
Fiberbots: Robotic fibers for high-precision minimally invasive surgery
Authors: Abdelaziz Mohamed E. M. K. , Zhao Jinshi , Rosa Bruno Gil , Lee Hyun-Taek , Simon Daniel , Vyas Khushi , Li Bing , Koguna Hanifa , Li Yue , Demircali Ali Anil , Uvet Huseyin , Gencoglan Gulsum , Akcay Arzu , Elriedy Mohamed , Kinross James , Dasgupta Ranan , Takats Zoltan , Yeatman Eric , Yang Guang-Zhong , Temelkuran Burak
Published: February 2023

Technologies that rely on the fundamental principle of thermal expansion have demonstrated high-precision, a growing demand in fields driven by miniaturization. However, scalable production of high aspect ratio devices that harness this capability while facilitating flexibility in design and functionality remains a challenge. We employed the high-throughput fiber thermal drawing technique to readily fabricate multimaterial fiberbots that can precisely and omnidirectionally move by asymmetric thermal expansion. These millimeter-scale fibers (< 2 mm) show excellent repeatability and linearity, negligible hysteresis, and can achieve micron-level resolution over four orders of magnitude motion range. By integrating these robotic fibers with medical devices that can perform cellular-level tissue imaging, diagnosis, and manipulation, we showcase their versatility through benchtop and preclinical animal studies and their overall potential impact on medicine, biomedical engineering, robotics, and beyond.

One Sentence Summary

Scalable manufacturing and integration of robotic fibers that deliver high-precision motion when heated.
Identification of major quantitative trait loci for parthenocarpic ability in East Asian melon
Authors: Yoshioka Yosuke , Nashiki Akito , Zaelani Ahmad , Isobe Sachiko , Shirasawa Kenta , Shimomura Koichiro , Ohyama Akio
Published: February 2023

Natural (genetic) parthenocarpy contributes to fruit yield and quality under unfavorable environmental conditions where there are no effective pollinators or fertile pollen grains. Several old melon cultivars and weedy melon in East Asia are known to have strong parthenocarpic ability, but there has been little progress in intentionally introducing this ability into current F1hybrid cultivars. Here, we examined its inheritance and confirmed the selection accuracy of DNA markers linked to it. We conducted QTL analysis using three F2populations derived from crosses between a non-parthenocarpic cultivar and three parthenocarpic accessions, and detected two major QTLs on chromosomes 2 (par2.1) and 3 (par3.1). The parthenocarpic parent allele at both QTLs enhanced parthenocarpic ability. Phenotypic segregation was well explained bypar2.1andpar3.1in two F2populations derived from Japanese weedy melon and an old Korean cultivar and bypar3.1in one from an old Japanese cultivar. This difference suggests that the effects ofpar2.1andpar 3.1depend on genetic background. Both QTL regions contain several phytohormone-related genes, so we randomly selected SNPs in auxin- and ethylene-related genes to confirm the accuracy of selection for parthenocarpic ability. These SNP markers proved sufficient, though not perfect, to select plants with strong parthenocarpic ability. These results provide new insights into the molecular mechanisms of parthenocarpic ability in melon and will contribute to the development of new cultivars with high parthenocarpic ability.

Key message

Several oriental melons have strong parthenocarpic ability controlled by one or two loci. DNA markers linked to these loci can select individuals with this ability.
Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes?
Authors: Lenormand Thomas , Roze Denis
Published: February 2023

Y and W chromosomes often stop recombining and degenerate. Most work on recombination suppression has focused on the mechanisms favoring recombination arrest in the short term. Yet, the long-term maintenance of recombination suppression is critical to evolving degenerate sex chromosomes. This long-term maintenance has been little investigated. In the long term, recombination suppression may be maintained for selective reasons (e.g., involving the emergence of nascent dosage compensation), or due to mechanistic constraints preventing the reestablishment of recombination, for instance when complex chromosomal rearrangements evolve on the Y. In this paper, we investigate these ‘constraint’ theories. We show that they face a series of theoretical difficulties: they are not robust to extremely low rates of recombination restoration; they would rather cause population extinction than Y degeneration; they are less efficient at producing a non-recombining and degenerate Y than scenarios adding a selective pressure against recombination, whatever the rate of recombination restoration. Finally, whether such very high constraints exist is questionable. Very low rates of recombination reestablishment are sufficient to prevent Y degeneration, given the large fitness advantage to recover a non-degenerate Y or W for the heterogametic sex. The assumption of a lack of genetic variation to restore recombination seems also implausible given known mechanisms to restore a recombining pair of sex chromosomes.
Precise and efficient C-to-U RNA Base Editing with SNAP-CDAR-S
Authors: Latifi Ngadhnjim , Mack Aline Maria , Tellioglu Irem , Di Giorgio Salvatore , Stafforst Thorsten
Published: February 2023

Site-directed RNA base editing enables the transient and dosable change of genetic information and represents a recent strategy to manipulate cellular processes, paving ways to novel therapeutic modalities. While tools to introduce adenosine-to-inosine changes have been explored quite intensively, the engineering of precise and programmable tools for cytidine-to-uridine editing is somewhat lacking behind. Here we demonstrate that the cytidine deaminase domain evolved from the ADAR2 adenosine deaminase, taken from the RESCUE-S tool, provides very efficient and highly programmable editing when changing the RNA targeting mechanism from Cas13-based to SNAP-tag-based. Optimization of the guide RNA chemistry further allowed to dramatically improve editing yields in the difficult-to-edit 5’-CCN sequence context thus improving the substrate scope of the tool. Regarding editing efficiency, SNAP-CDAR-S outcompeted the RESCUE-S tool clearly on all tested targets, and was highly superior in perturbing the β-catenin pathway. NGS analysis showed similar, moderate global off-target A-to-I and C-to-U editing for both tools.
Optogenetic urothelial cell stimulation induces bladder contractions and pelvic nerve afferent firing
Authors: Robilotto Gabriella L , Yang Olivia J , Alom Firoj , Johnson Richard D , Mickle Aaron D
Published: February 2023

Urothelial cells, which play an essential role in the barrier function, are also thought to play a sensory role in bladder physiology by releasing signaling molecules in response to sensory stimuli that act upon adjacent sensory neurons. However, it is challenging to study this communication due to the overlap in receptor expression and proximity of urothelial cells to sensory neurons. To overcome this challenge, we have developed a mouse model where we can directly stimulate urothelial cells using optogenetics. We have crossed a uroplakin II-cre mouse (UPK2-Cre) with a mouse that expresses the light-activated cation channel, Channelrhodopsin-2 (ChR2), in the presence of cre-expression. Optogenetic stimulation of urothelial cells cultured from UPK2-ChR2 initiates cellular depolarization and release of adenosine triphosphate. Cystometry recordings demonstrate that optical stimulation of urothelial cells increases bladder pressure and pelvic nerve activity. Increases in bladder pressure persisted, albeit to a lesser extent, when the bladder was excised in anin vitropreparation. The P2X receptor antagonist, PPADS, significantly reduced optically evoked bladder contractionsin vivoandex vivo. Further, corresponding nerve activity was also inhibited with PPADS. Our data suggest that urothelial cells can initiate robust bladder contractions via sensory nerve signaling or contractions through local signaling mechanisms. This data supports a foundation of literature demonstrating communication between sensory neurons and urothelial cells. Importantly, with further use of these optogenetic tools, we hope to scrutinize this signaling mechanism, its importance for normal micturition and nociception, and how it may be altered in pathophysiologic conditions.

Animal Studies

All the procedures involving mice and mouse tissue performed in this study were approved by the University of Florida Institutional Animal Care and Use Committee and in strict accordance with the US National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals.

Significance

It has been appreciated for almost two decades that urothelial cells play a sensory role in bladder function. However, it has been particularly challenging to study this communication as both sensory neurons, and urothelial cells express the same sensory receptors. Here we demonstrate an optogenetic technique to specifically stimulate urothelial cells and evaluate the effects on bladder physiology. We used this technique to show that specific urothelial stimulation resulted in bladder contractions. This approach will have a long-lasting impact on how we study urothelial-to-sensory neuron communication and the changes that occur under disease conditions.
Macrophage-targeted lipid nanoparticle delivery of microRNA-146a to mitigate hemorrhagic shock-induced acute respiratory distress syndrome
Authors: Fei Qinqin , Shalosky Emily M. , Barnes Ryelie , Shukla Vasudha C. , Ballinger Megan N. , Farkas Laszlo , Lee Robert J. , Ghadiali Samir N. , Englert Joshua A.
Published: February 2023

The pro-inflammatory response of alveolar macrophages to injurious physical forces during mechanical ventilation is regulated by the anti-inflammatory microRNA, miR-146a. Increasing miR-146a expression to supraphysiologic levels using untargeted lipid nanoparticles reduces ventilator-induced lung injury, but requires a high initial dose of miR-146a making it less clinically applicable. In this study, we developed mannosylated lipid nanoparticles that can effectively mitigate lung injury at the initiation of mechanical ventilation with lower doses of miR-146a. We used a physiologically relevant humanizedin vitroco-culture system to evaluate the cell-specific targeting efficiency of the mannosylated lipid nanoparticle. We discovered that mannosylated lipid nanoparticles preferentially deliver miR-146a to alveolar macrophages and reduce force-induced inflammationin vitro. Ourin vivostudy using a clinically relevant mouse model of hemorrhagic shock-induced acute respiratory distress syndrome demonstrated that delivery of a low dose miR-146a (0.1 nmol) using mannosylated lipid nanoparticles dramatically increases miR-146a in mouse alveolar macrophages and decreases lung inflammation. These data suggest that mannosylated lipid nanoparticles may have therapeutic potential to mitigate lung injury during mechanical ventilation.
Small-molecule targeting of GPCR-independent non-canonical G protein signaling inhibits cancer progression
Authors: Zhao Jingyi , DiGiacomo Vincent , Ferreras-Gutierrez Mariola , Dastjerdi Shiva , de Opakua Alain Ibáñez , Park Jong-Chan , Luebbers Alex , Chen Qingyan , Beeler Aaron , Blanco Francisco J , Garcia-Marcos Mikel
Published: February 2023

Activation of heterotrimeric G-proteins (Gαβγ) by G-protein-coupled receptors (GPCRs) is a quintessential mechanism of cell signaling widely targeted by clinically-approved drugs. However, it has become evident that heterotrimeric G-proteins can also be activated via GPCR-independent mechanisms that remain untapped as pharmacological targets. GIV/Girdin has emerged as a prototypical non-GPCR activator of G proteins that promotes cancer metastasis. Here, we introduce IGGi-11, a first-in-class smallmolecule inhibitor of non-canonical activation of heterotrimeric G-protein signaling. IGGi-11 binding to G-protein α-subunits (Gαi) specifically disrupted their engagement with GIV/Girdin, thereby blocking non-canonical G-protein signaling in tumor cells, and inhibiting pro-invasive traits of metastatic cancer cellsin vitroand in mice. In contrast, IGGi-11 did not interfere with canonical G-protein signaling mechanisms triggered by GPCRs. By revealing that small molecules can selectively disable non-canonical mechanisms of G-protein activation dysregulated in disease, these findings warrant the exploration of therapeutic modalities in G-protein signaling that go beyond targeting GPCRs.
Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition
Authors: Li Xuanji , Brejnrod Asker , Trivedi Urvish , Russel Jakob , Stokholm Jakob , Thorsen Jonathan , Shah Shiraz A , Vestergaard Gisle Alberg , Rasmussen Morten Arendt , Nesme Joseph , Bisgaard Hans , Sørensen Søren Johannes
Published: February 2023

Even in the absence of antibiotic exposure, the gut microbiome of infants has been shown to contain numerous antibiotic resistance genes (ARGs), but the mechanism for this remains unclear. In environmental bacteria, the selective advantage of ARGs can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes. However, this phenomenon is unknown from the human gut microbiome during early life despite frequent exposures to biocides and metals from an early age. Here, we conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity, especiallyE. coli. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes located near other ARGs, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of virulence genes was associated with low gut microbial maturity and that virulence genes showed even higher potential for mobility than ARGs. Our study highlights important constraints that need to be considered when developing strategies to combat ARG dissemination.
Microtubule binding of the human HAUS complex is directly controlled by importins and Ran-GTP
Authors: Ustinova Kseniya , Ruhnow Felix , Gili Maria , Surrey Thomas
Published: February 2023

Mitotic spindle assembly during cell division is a highly regulated process. Ran-GTP produced around chromosomes controls the activity of a multitude of spindle assembly factors by releasing them from inhibitory interaction with importins. A major consequence of Ran-GTP regulation is the stimulation of local microtubule nucleation around chromosomes via augmin/HAUS-mediated branched microtubule nucleation, a process that is critically important for correct spindle assembly. However, augmin is not known to be a direct target of the Ran-GTP pathway, raising the question of how its activity is controlled. Here we present thein vitroreconstitution of Ran-GTP-regulated microtubule binding of the human HAUS complex. We demonstrate that importins directly bind to the HAUS complex, which prevents HAUS from binding to microtubules. Ran-GTP relieves this inhibition. Therefore, the HAUS complex is a direct target of the Ran-GTP pathway, suggesting that branching microtubule nucleation is directly regulated by the Ran-GTP gradient around chromosomes in dividing cells.
Aerobic anoxygenic phototrophic bacteria are ubiquitous in phyllo- and endosphere microbiomes of boreal and subarctic plants
Authors: Nissinen Riitta , Franz Ole , Kovanen Salla , Mäkelä Meri , Kraft Venla , Ketola Katri , Liukkonen Alli , Heikkilä-Huhta Kati , Häkkänen Heikki , Ihalainen Janne A.
Published: February 2023

In addition to oxygenic photosynthetic systems, solar radiation is utilized for energy by diverse anoxygenic photosynthetic systems. Aerobic anoxygenic phototrophic bacteria (AAPB) perform photosynthesis without producing oxygen but still live in aerobic conditions. Typically they have been reported from aquatic ecosystems, but they can also be found from polar and desert soil ecosystems and primary succession communities like soil crusts. Recently, AAPB have been discovered in the metagenomic data of several plant phyllospheres. By utilizing citizen science, we screened plant foliar samples from eleven different locations in Finland for AAPB by near infrared fluorescence imaging of culturable phyllosphere and endosphere bacteria. Near infrared fluorescence reports the presence of AAPB which contain Bacteriochlorophyllamolecules, embedded in Light Harvesting 1 - Reaction Center complex. We found that AAPB were ubiquotous in phyllosphere communities of diverse plant species in all sampling locations. They were also consistently present in the endosphere of plant species with perennial leaves. Most of the AAPB isolated represent alphaproteobacterial genera Sphingomonas and Methylobacterium, but several isolates from genus Lichenihabitans as well as putative novel alphaproteobacterial taxa were also identified. Methylobacterial isolates were mostly detected in the phyllosphere with weak host specificity, while Sphingomonas AAPB were detected also in the endosphere of several plant species, with clear host specific taxa. We studied also the fluorescence spectral properties of several AAPBs. All the observed spectra resemble typical fluorescence spectral properties of Light Harvesting complex 1. Still, slight variation among each spectra could be obtained, revealing some physical difference among the complexes. Our results demonstrate for the first time, that AAPB are common in cold climate plant endophytic as well as epiphytic microbiomes and they build up substantial amounts of Bacteriochlorophyllacontaining Light Harvesting complexes. Their putative role in plant adaptation to strong seasonality in light and temperature or tolerance of abiotic stressors remains to be investigated in future studies.
Geographic and seasonal variation of theforgene reveal signatures of local adaptation inDrosophila melanogaster
Authors: Perez Dylan J. Padilla
Published: February 2023

In the early 1980s, the observation thatDrosophila melanogasterlarvae differed in their foraging behavior laid the foundation for the work that would later lead to the discovery of the foraging gene (for) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of theforgene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying adaptation of populations in response to environmental variation. Here, I present results of a genotype-environment association analysis that quantifies variation at theforgene among samples ofD. melanogasterstructured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based onFstvalues, and an analysis of population structure revealed an east-west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behavior inD. melanogaster.
Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring inEscherichia coli
Authors: Westlund Emma , Bergenstråle Axel , Pokhrel Alaska , Chan Helena , Skoglund Ulf , Daley Daniel O. , Söderström Bill
Published: February 2023

Understanding where proteins are localized in a bacterial cell is essential for understanding their function and regulation. This is particularly important for proteins that are involved in cell division, which localize at the division septum and assemble into highly regulated complexes. Current knowledge of these complexes has been greatly facilitated by super-resolution imaging using fluorescent protein fusions. Herein we demonstrate with FtsZ that single-molecule PALM images can be obtainedin-vivousing a genetically fused nanotag (ALFA) and a corresponding nanobody fused to mEos3.2. The methodology presented is applicable to other bacterial proteins.
Isolated nuclei from frozen tissue are the superior source for single cell RNA-seq compared with whole cells
Authors: Jiang Andrew , Lehnert Klaus , Reid Suzanne J. , Handley Renee R. , Jacobsen Jessie C. , Rudiger Syke R. , McLaughlan Clive J. , Verma Paul J. , Bawden C. Simon , Snell Russell G.
Published: February 2023

The isolation of intact single cells from frozen tissue is a challenge due to the mechanical and physical stress inflicted upon the cell during the freeze-thaw process. Ruptured cells release ambient RNA into the cell suspension, which can become encapsulated into droplets during droplet based single cell RNA-seq library preparation methods. The presence of ambient RNA in droplets has been suggested to impact data quality, however there have been limited reports on single cell RNA-seq data from frozen tissue. Here, we compare the results of single cell RNA-seq derived from disaggregated cells from frozen brain tissue with single nuclei RNA-seq derived from purified nuclei of identical tissue using the 10X Genomics Chromium 3’gene expression assay. Our results indicated that presence of ambient RNA in the cell suspension resulted in single cell RNA-seq data with a 25-fold lower gene count, a 5-fold lower UMI count per cell and a 2-fold lower fraction of reads per cell compared with single nuclei RNA-seq data. Cell clustering with the single cell RNA-seq data was unable to resolve the heterogeneity of brain cell types. Our conclusion is that nuclei from frozen tissue are the superior substrate for single cell transcriptome analysis.
Linguistic and attentional factors – not statistical regularities – contribute to word-selective neural responses with FPVS-oddball paradigms
Authors: Lochy Aliette , Rossion Bruno , Lambon-Ralph Matthew , Volfart Angélique , Hauk Olaf , Schiltz Christine
Published: February 2023

In recent years, a fast periodic oddball-like paradigm has proved to be highly sensitive to measure category-selective visual word representation and characterize its development and neural basis. In this approach, deviant words are inserted in rapid streams of base stimuli every nthoccurrence (e.g., Lochy et al., 2015). To understand the nature of word-selective representation and improve its measurement, we tested 22 adults with EEG, assessing the impact of discrimination coarseness (deviant words among nonwordsorpseudowords), the relative frequency of item repetition (set sizeoritem repetition controlled for deviant vs. base stimuli), and the nature of the orthogonal attentional task (focused or deployed spatial attention). In all stimulation sequences, base stimuli were presented at 10 Hz, with words inserted every 5 stimuli generating word-selective responses in the EEG spectra at 2 Hz and harmonics. Word-selective occipito-temporal responses were robust at the individual level, left-lateralized and sensitive to wordlikeness of base stimuli, being stronger in the coarser categorical contrast (among nonwords). Amplitudes were not affected by item repetition, showing that implicit statistical learning about a relative token frequency difference for deviant stimuli does not contribute to the word-selective neural activity, at least with relatively large stimulus set sizes (n=30). Finally, the broad attentional deployment task produced stronger responses than a focused task, an important finding for future studies in the field. Taken together, these results confirm the linguistic nature of word-selective responses, strengthen the validity and increase the sensitivity of the FPVS-EEG oddball paradigm to measure visual word recognition.

Highlights

Word-selective responses measured in fast periodic visual stimulation with EEG are linguistic in nature

Word-selective responses reflect prelexical or lexical processes depending on the contrast (words in nonwords or pseudowords respectively)

Using sufficiently large sets (30 items) prevents the extraction of statistical regularities and hence, statistical learning

Using an orthogonal task involving broad, rather than focused, spatial attention increases amplitude of the neural responses

Sensitivity of the paradigm to detect significant responses at the individual level is very good (95% for prelexical and about 80% for lexical word responses)
DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular environments
Authors: Costello Whitney N. , Xiao Yiling , Mentink-Vigier Frederic , Kragelj Jaka , Frederick Kendra K.
Published: February 2023

With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition we find that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7
Authors: Prolič-Kalinšek Maruša , Volkov Alexander N. , Hadži San , Van Dyck Jeroen , Bervoets Indra , Charlier Daniel , Loris Remy
Published: February 2023

YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA-binding protein and recognizes a 5′-TTGATTN6AATCAA-3′ inverted repeat. The DNA-binding domain is a helix–turn–helix (HTH)-containing POU domain and is followed by a long α-helix (α6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α2 and the recognition helix α3 in the HTH motif is unusually long compared with typical HTH motifs, and is highly variable in sequence and length within the YdaT family. The POU domains have a large degree of freedom to move relative to the helix bundle in the free structure, but their orientation becomes fixed upon DNA binding.
Epidemiology and comorbidity of hidradenitis suppurativa in Korea for 17 years: A nationwide population‐based cohort study
Authors: Lee Jong Won , Heo Yeon‐Woo , Lee Ji Hae , Lee Solam
Published: February 2023

Hidradenitis suppurativa (HS) is associated with various metabolic and autoimmune diseases. The epidemiology has been analyzed in various studies worldwide. However, epidemiological data on HS for Asian populations are limited. This study aimed to analyze the change in the prevalence and incidence of HS over 17 years in South Korea using the Korean National Health Insurance Service (NHIS) database. This study also evaluated the comorbidities in patients with HS. Population‐based data from the NHIS database of Korea were obtained between January 2003 and December 2019. Odds ratios were estimated to determine the association between comorbidities and HS during the study period. Hazard ratios for the risk of incident comorbidities in patients with HS were obtained using the multivariable Cox proportional hazard analysis. This study included 45 511 patients with HS and 910 220 controls matched for age, sex, insurance type, and income level. The incidence rate of HS per 1 000 000 person‐years in Korea increased from 11.69 in 2003 to 78.78 in 2019. The annual prevalence per 1 000 000 people also increased from 34.68 in 2003 to 140.10 in 2019, showing a similar trend. Many comorbidities, including atopic, metabolic and end‐organ, autoimmune/inflammatory, and psychiatric diseases were associated with HS at baseline. In many diseases, the risk of incident comorbidities in patients with HS was higher than that in controls. The incidence and prevalence of HS in Korea have increased over the past 17 years. Various comorbidities, including allergic diseases, hypertension, diabetes mellitus, dyslipidemia, myocardial infarction, chronic hepatitis and cirrhosis, chronic kidney disease, inflammatory bowel diseases, rheumatoid arthritis, vitamin D deficiency, and psychiatric diseases, were associated with HS. Physicians need to keep in mind and closely monitor these comorbidities in patients with HS.
Digitalization and inclusiveness of HRM practices: The example of neurodiversity initiatives
Authors: Walkowiak Emmanuelle
Published: February 2023

The transformation of the intelligence ecosystem associated with the digital transformation represents a critical juncture for diversity and inclusion (D&I). We present a multidisciplinary perspective on digital transformation and D&I that demonstrates that, in the context of automated decision making, where algorithmic biases and the standardisation of thought represent new risks, neurodiversity initiatives become a cornerstone for advancing D&I. Based on interviews with neurodiversity experts, we identify innovative ways to efficiently configure an inclusive organisational design targeting neurodiversity by leveraging technologies. We identify several properties of technologies that support D&I in neurodiversity initiatives: the neutralisation of biases during interviews, the development of digital support for physical and mental well‐being and the facilitation of different cognition modes. Finally, we critically discuss the risks and opportunities offered by various technologies in terms of performance evaluation, new forms of dominance, and design of a digital ecosystem for mental well‐being.
Improved health‐related quality of life after hepatitis C viraemic clearance among people who inject drugs may not be durable
Authors: McDonald Scott A. , Myring Gareth , Palmateer Norah E. , McAuley Andrew , Beer Lewis , Dillon John F. , Hollingworth William , Gunson Rory , Hickman Matthew , Hutchinson Sharon J.
Published: February 2023

Background and Aims

Chronic infection with the hepatitis C virus (HCV) has a detrimental impact on health‐related quality of life (QoL). Scale‐up of HCV direct‐acting antiviral (DAA) therapy among people who inject drugs (PWID) is underway in several countries since the introduction of interferon‐free regimens. This study aimed to assess the impact of DAA treatment success on QoL for PWID.

Design

Cross‐sectional study using two rounds of the Needle Exchange Surveillance Initiative, a national anonymous bio‐behavioural survey and a longitudinal study involving PWID who underwent DAA therapy.

Setting

The setting for the cross‐sectional study was Scotland (2017–2018, 2019–2020). The setting for the longitudinal study was the Tayside region of Scotland (2019–2021).

Participants

In the cross‐sectional study PWID were recruited from services providing injecting equipment (n = 4009). In the longitudinal study, participants were PWID on DAA therapy (n = 83).

Measurements

In the cross‐sectional study, the association between QoL (measured using the EQ‐5D‐5L quality of life instrument) and HCV diagnosis and treatment was assessed using multilevel linear regression. In the longitudinal study, QoL was compared at four timepoints using multilevel regression, from treatment commencement until 12 months following commencement.

Findings

In the cross‐sectional study, 41% (n = 1618) were ever chronically HCV infected, of whom 78% (n = 1262) were aware of their status and of whom 64% (n = 704) had undergone DAA therapy. There was no evidence for a marked QoL improvement associated with viral clearance among those treated for HCV (B = 0.03; 95% CI, −0.03 to 0.09). In the longitudinal study, improved QoL was observed at the sustained virologic response test timepoint (B = 0.18; 95% CI, 0.10–0.27), but this was not maintained at 12 months following start of treatment (B = 0.02; 95% CI, −0.05 to 0.10).

Conclusions

Successful direct‐acting antiviral therapy for hepatitis C infection may not lead to a durable improvement in quality of life among people who inject drugs, although there may be a transient improvement around the time of sustained virologic response. Economic models of the impact of scaling‐up treatment may need to include more conservative quality of life benefits over and above reductions in mortality, disease progression and transmission of infection.
How do patients feel during the first 72 h after initiating long‐acting injectable buprenorphine? An embodied qualitative analysis
Authors: Neale Joanne , Parkin Stephen , Strang John
Published: February 2023

Background and Aims

Long‐acting injectable buprenorphine (LAIB) is a new treatment for opioid use disorder that is generating positive outcomes. Negative effects are typically mild and transient, but can occasionally be serious, resulting in treatment discontinuation/non‐adherence. This paper aims to analyse patients’ accounts of how they felt during the first 72 h after initiating LAIB.

Methods

Semi‐structured interviews were conducted (June 2021–March 2022) with 26 people (18 males and 8 females) who had started LAIB within the previous 72 h. Participants were recruited from treatment services in England and Wales and were interviewed by telephone using a topic guide. Interviews were audio‐recorded, transcribed and coded. The concepts of embodiment and embodied cognition framed the analyses. Data on participants’ substance use, initiation onto LAIB and feelings were tabulated. Next, participants’ accounts of how they felt were analysed following the stages of Iterative Categorization.

Results

Participants reported complex combinations of changing negative and positive feelings. Bodily experiences included withdrawal symptoms, poor sleep, injection‐site pain/soreness, lethargy and heightened senses inducing nausea (‘distressed bodies’), but also enhanced somatic wellbeing, improved sleep, better skin, increased appetite, reduced constipation and heightened senses inducing pleasure (‘returning body functions’). Cognitive responses included anxiety, uncertainties and low mood/depression (‘the mind in crisis’) and improved mood, greater positivity and reduced craving (‘feeling psychologically better’). Whereas most negative effects reported are widely recognized, the early benefits of treatment described are less well‐documented and may be an overlooked distinctive feature of LAIB.

Conclusions

During the first 72 h after initiating long‐acting injectable buprenorphine, new patients report experiencing a range of interconnected positive and negative short‐term effects. Providing new patients with information about the range and nature of these effects can prepare them for what to expect and help them manage feelings and reduce anxiety. In turn, this may increase medication adherence.
Combined uterorelaxant effect of magnesium sulfate and terbutaline: Studies on late pregnant rat uteri in vitro and in vivo
Authors: Barna Tamara , Szucs Kalman F. , Schaffer Annamaria , Mirdamadi Mohsen , Hajagos‐Toth Judit , Gaspar Robert
Published: February 2023

Introduction

Preterm delivery and its complications are among the biggest challenges and health risks in obstetrical practice. Several tocolytic agents are used in clinical practice, although the efficacy and side effect profiles of these drugs are not satisfying. The aim of this study was to investigate the uterus relaxant effect of the coadministration of β2‐mimetic terbutaline and magnesium sulfate (MgSO4) in an isolated organ bath and to perform in vivo smooth muscle electromyographic (SMEMG) studies in pregnant rats. In addition, we also investigated whether the tachycardia‐inducing effect of terbutaline can be reduced by the presence of magnesium, due to the opposite heart rate modifying effects of the two agents.

Material and methods

In the isolated organ bath studies, rhythmic contractions of 22‐day‐ pregnant Sprague–Dawley rats were stimulated with KCl, and cumulative dose–response curves were constructed in the presence of MgSO4 or terbutaline. The uterus‐relaxing effects of terbutaline were also investigated in the presence of MgSO4 in both normal buffer and Ca2+‐poor buffer. The in vivo SMEMG studies were carried out under anesthesia with the subcutaneous implantation of an electrode pair. The animals were treated with MgSO4 or terbutaline alone or in combination in a cumulative bolus injection. The implanted electrode pair also detected the heart rate.

Results

Both MgSO4 and terbutaline reduced uterine contractions in vitro and in vivo, furthermore, the administration of a small dose of MgSO4 significantly enhanced the relaxant effect of terbutaline, especially in the lower range. However, in Ca2+‐poor environment, MgSO4 was not able to increase the effect of terbutaline, indicating the role of MgSO4 as a Ca2+ channel blocker. In the cardiovascular studies, MgSO4 significantly decreased the tachycardia‐inducing effect of terbutaline in late pregnant rats.

Conclusions

The combined application of MgSO4 and terbutaline may have clinical significance in tocolysis, which must be confirmed in clinical trials. Furthermore, MgSO4 could substantially reduce the tachycardia‐inducing side effect of terbutaline.
Childhood sleep health and epigenetic age acceleration in late adolescence: Cross‐sectional and longitudinal analyses
Authors: Balfour David , Melton Phillip E. , McVeigh Joanne A. , Huang Rae‐Chi , Eastwood Peter R. , Wanstall Sian , Reynolds Amy C. , Cohen‐Woods Sarah
Published: February 2023

Aim

Investigate if childhood measures of sleep health are associated with epigenetic age acceleration in late adolescence.

Methods

Parent‐reported sleep trajectories from age 5 to 17, self‐reported sleep problems at age 17, and six measures of epigenetic age acceleration at age 17 were studied in 1192 young Australians from the Raine Study Gen2.

Results

There was no evidence for a relationship between the parent‐reported sleep trajectories and epigenetic age acceleration (p ≥ 0.17). There was a positive cross‐sectional relationship between self‐reported sleep problem score and intrinsic epigenetic age acceleration at age 17 (b = 0.14, p = 0.04), which was attenuated after controlling for depressive symptom score at the same age (b = 0.08, p = 0.34). Follow‐up analyses suggested this finding may represent greater overtiredness and intrinsic epigenetic age acceleration in adolescents with higher depressive symptoms.

Conclusion

There was no evidence for a relationship between self‐ or parent‐reported sleep health and epigenetic age acceleration in late adolescence after adjusting for depressive symptoms. Mental health should be considered as a potential confounding variable in future research on sleep and epigenetic age acceleration, particularly if subjective measures of sleep are used.