bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotype-based single-cell transcriptomics reveal compensatory pathways involved in Golgi organization and associated transport
Authors: Singh Sanjana , Zukowska Joanna , Halavatyi Aliaksandr , Landry Jonathan J. M. , Pepperkok Rainer
Published: December 2022

The Golgi is a dynamic organelle with a unique morphology that has implications on its function. How the structural integrity of the Golgi is maintained despite its dynamic nature has been a long-standing question. Several siRNA-based screens have addressed this question and have identified a number of key players required for Golgi integrity. Interestingly, they also reported heterogeneity of phenotypic responses with regards to Golgi morphology. Although never systematically investigated, this variability has generally been attributed to poor transfection efficiency or cell cycle specific responses. Here we show that this heterogeneity is the result of differential response to the siRNA knockdown in different Golgi phenotypes, independent of transfection efficiency or cell cycle phases. To characterize the observed Golgi phenotype-specific responses at the molecular level we have developed an automated assay which enables microscopy-based phenotype classification followed by phenotype-specific single-cell transcriptome analysis. Application of this novel approach to the siRNA mediated knockdown of USO1, a key trafficking protein at the ER to Golgi boundary, surprisingly suggests a key involvement of the late endosomal/endocytic pathways in the regulation of Golgi organization. Our pipeline is the first of its kind developed to study Golgi organization, but can be applied to any biological problem that stands to gain from correlating morphology with single-cell readouts. Moreover, its automated and modular nature allows for uncomplicated scaling up, both in throughput and in complexity, helping the user achieve a systems level understanding of cellular processes.
Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data
Authors: Helekal David , Keeling Matt , Grad Yonatan H , Didelot Xavier
Published: December 2022

Increasing levels of antibiotic resistance in many bacterial pathogen populations is a major threat to public health. Resistance to an antibiotic provides a fitness benefit when the bacteria is exposed to this antibiotic, but resistance also often comes at a cost to the resistant pathogen relative to susceptible counterparts. We lack a good understanding of these benefits and costs of resistance for many bacterial pathogens and antibiotics, but estimating them could lead to better use of antibiotics in a way that reduces or prevents the spread of resistance. Here, we propose a new model for the joint epidemiology of susceptible and resistant variants, which includes explicit parameters for the cost and benefit of resistance. We show how Bayesian inference can be performed under this model using phylogenetic data from susceptible and resistant lineages and that by combining data from both we are able to disentangle and estimate the resistance cost and benefit parameters separately. We applied our inferential methodology to several simulated datasets to demonstrate good scalability and accuracy. We analysed a dataset ofNeisseria gonorrhoeaegenomes collected between 2000 and 2013 in the USA. We found that two unrelated lineages resistant to fluoroquinolones shared similar epidemic dynamics and resistance parameters. Fluoroquinolones were abandoned for the treatment of gonorrhoea due to increasing levels of resistance, but our results suggest that they could be used to treat a minority of around 10% of cases without causing resistance to grow again.
Molecular signatures of alternative fitness strategies in a facultatively social hover wasp
Authors: Taylor Benjamin A. , Taylor Daisy , Bodrug-Schepers Alexandrina , Câmara Ferreira Francisco , Stralis-Pavese Nancy , Himmelbauer Heinz , Guigó Roderic , Reuter Max , Sumner Seirian
Published: December 2022

Social insect queens and workers represent ideal models with which to understand the expression and regulation of alternative reproductive phenotypes. Most research in this area has focused on the molecular regulation of reproductive castes in obligately social taxa with complex social systems, while relatively few studies have addressed the molecular basis of caste in species in which the division of reproductive labour is more plastic. As a result, it is not clear whether, and to what extent, the mechanisms of caste in species with reproductive plasticity are the same as those that exist at the highest levels of social complexity. To address this knowledge gap, we analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social hover wasp Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive ‘queues’ exhibited by social groups of this species, we show that reproductive division of labour in this species is associated with surprisingly distinct transcriptomic signatures, similar to those observed in more complex social taxa; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that distinct co-expressed gene sets are associated with differential investment into alternative reproductive strategies. These results elucidate robust transcriptomic signals that represent the proximate basis of division of labour at the simplest level of insect sociality, and show these signals to be remarkably similar to those in more derived species.
Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers
Authors: Eldjárn Hjörleifsson Kristján , Sullivan Delaney K. , Swarna Nikhila P. , Holley Guillaume , Melsted Páll , Pachter Lior
Published: December 2022

In single-cell and single-nucleus RNA sequencing, the coexistence of nascent (unprocessed) and mature (processed) mRNA poses challenges in accurate read mapping and the interpretation of count matrices. The traditional transcriptome reference, defining the ‘region of interest’ in bulk RNA-seq, restricts its focus to mature mRNA transcripts. This restriction leads to two problems: reads originating outside of the ‘region of interest’ are prone to mismapping within this region, and additionally, such external reads cannot be matched to specific transcript targets. Expanding the ‘region of interest’ to encompass both nascent and mature mRNA transcript targets provides a more comprehensive framework for RNA-seq analysis. Here, we introduce the concept of distinguishing flankingk-mers (DFKs) to improve mapping of sequencing reads. We have developed an algorithm to identify DFKs, which serve as a sophisticated ‘background filter’, enhancing the accuracy of mRNA quantification. This dual strategy of an expanded region of interest coupled with the use of DFKs enhances the precision in quantifying both mature and nascent mRNA molecules, as well as in delineating reads of ambiguous status.
Posterior marginalization accelerates Bayesian inference for dynamical systems
Authors: Raimúndez Elba , Fedders Michael , Hasenauer Jan
Published: December 2022

Bayesian inference is an important method in the life and natural sciences for learning from data. It provides information about parameter uncertainties, and thereby the reliability of models and their predictions. Yet, generating representative samples from the Bayesian posterior distribution is often computationally challenging. Here, we present an approach that lowers the computational complexity of sample generation for problems with scaling, offset and noise parameters. The proposed method is based on the marginalization of the posterior distribution, which reduces the dimensionality of the sampling problem. We provide analytical results for a broad class of problems and show that the method is suitable for a large number of applications. Subsequently, we demonstrate the benefit of the approach for various application examples from the field of systems biology. We report a substantial improvement up to 50 times in the effective sample size per unit of time, in particular when applied to multi-modal posterior problems. As the scheme is broadly applicable, it will facilitate Bayesian inference in different research fields.
Waterlogging shifts ontogenic hormone dynamics in tomato leaves and petioles
Authors: Geldhof B. , Novák O. , Van de Poel B.
Published: December 2022

Waterlogging leads to hypoxic conditions in the root zone that subsequently cause systemic adaptive responses in the shoot, including leaf epinasty. Waterlogging-induced epinasty in tomato has long been ascribed to the coordinated action of ethylene and auxins. However, other hormonal signals have largely been neglected, despite evidence of their importance in leaf posture control. To adequately cover a large group of growth regulators, we performed a tissue-specific and time-dependent hormonomics analysis. This analysis revealed that multiple hormones are differentially affected throughout a 48 h waterlogging treatment, and, more importantly, that leaf development defines a framework in which this hormonal control is regulated. In addition, we could distinguish early hormonal signals that might contribute to fast responses towards oxygen deprivation from those that potentially sustain the waterlogging response. For example, abscisic acid (ABA) levels peak in petioles within the first 12 h of the treatment, while its metabolites only rise much later, suggesting ABA transport is altered. At the same time, cytokinins (CK) and their derivatives drastically decline during waterlogging in leaves of all ages. This drop in CK possibly releases the inhibition of ethylene and auxin mediated cell elongation to establish epinastic bending. Auxins themselves rise substantially in the petiole of mature leaves, but mostly after 48 h of root hypoxia. Based on our hormone profiling, we propose that ethylene and ABA might act synergistically to dynamically fine-tune the balance of IAA and CK in the petiole, ultimately leading to differential growth and epinasty during waterlogging.
The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression
Authors: Peede David , Ortega-Del Vecchyo Diego , Huerta-Sánchez Emilia
Published: December 2022

The past decade has ushered in a resurgence of studies highlighting the importance of introgression throughout the Tree of Life. Several methods exist for detecting and quantifying introgression on a genomic scale, yet the majority of these methods primarily utilize signals of derived allele sharing between donor and recipient populations. In this study, we exploit the fact that introgression will not only result in derived allele sharing but also the reintroduction of ancestral alleles to derive new estimators of the admixture proportion. Using coalescent simulations, we assess the performance of our new methods and the methods proposed inLopez Fang et al. 2022to assess the utility of incorporating shared ancestral variation into genome-wide inferences of introgression. Using coalescent theory, simulations, and applying our methods to human and canid data, we find that methods incorporating ancestral allele sharing are comparable to their derived allele sharing counterparts, in turn providing researchers with the opportunity to utilize more of the genomic signature of introgression.
From a different angle: genetic diversity underlies differentiation of waterlogging-induced epinasty in tomato
Authors: Geldhof B. , Pattyn J. , Van de Poel B.
Published: December 2022

In tomato, downward leaf bending is a morphological adaptation towards waterlogging, which has been shown to induce a range of metabolic and hormonal changes. This kind of functional trait is often the result of a complex interplay of regulatory processes starting at the gene level, gated through a plethora of signaling cascades and modulated by environmental cues. Through phenotypical screening of a population of 54 tomato accessions in a Genome Wide Association Study (GWAS), we have identified target genes potentially involved in plant growth and survival during waterlogging and subsequent recovery. Changes in both plant growth rate and epinastic descriptors revealed several associations to genes possibly supporting metabolic activity in low oxygen conditions in the root zone. In addition to this general reprogramming, some of the targets were specifically associated to leaf angle dynamics, indicating these genes might play a role in the induction, maintenance or recovery of differential petiole elongation in tomato during waterlogging.
Higher-order thalamic nuclei facilitate the generalization and maintenance of spike-and-wave discharges of absence seizures
Authors: Atherton Zoe , Nagy Olivér , Barcsai Lívia , Sere Péter , Zsigri Nikolett , Földi Tamás , Berényi Antal , Crunelli Vincenzo , Lőrincz Magor L.
Published: December 2022

Spike-and-wave discharges (SWDs), generated by the cortico-thalamo-cortical (CTC) network, are pathological, large amplitude oscillations and the hallmark of absence seizures (ASs). SWDs begin in a cortical initiation network in both humans and animal models, including the Genetic Absence Epilepsy Rats from Strasbourg (GAERS), where it is located in the primary somatosensory cortex (S1). The behavioral manifestation of an AS occurs when SWDs spread from the cortical initiation site to the whole brain, however, the mechanisms behind this rapid propagation remain unclear. Here we investigated these processes beyond the principal CTC network, in higher-order (HO) thalamic nuclei (lateral posterior (LP) and posterior (PO) nuclei) since their diffuse connectivity and known facilitation of intracortical communications make these nuclei key candidates to support SWD generation and maintenance. In freely moving GAERS, multi-site LFP in LP, PO and multiple cortical regions revealed a novel feature of SWDs: during SWDs there are short periods (named SWD-breaks) when cortical regions far from S1, such the primary visual cortex (V1), become transiently unsynchronized from the ongoing EEG rhythm. Inactivation of HO nuclei with local muscimol injections or optogenetic perturbation of HO nuclei activity increased the occurrence of SWD-breaks and the former intervention also increased the SWD propagation-time from S1. The neural underpinnings of these findings were explored further by silicon probe recordings from single units of PO which uncovered two previously unknown groups of excitatory neurons based on their burst firing dynamics at SWD onset. Moreover, a switch from tonic to burst firing at SWD onset was shown to be an important feature since it was much less prominent for non-generalized events, i.e. SWDs that remained local to S1. Additionally, one group of neurons showed a reverse of this switch during SWD-breaks, demonstrating the importance of this firing pattern throughout the SWD. In summary, these results support the view that multiple HO thalamic nuclei are utilized at SWD onset and contribute to cortical synchrony throughout the paroxysmal discharge.
Sfp1 integrates TORC1 and PKA activity towards yeast ribosome biogenesis
Authors: Vuillemenot Luc-Alban , Ho Franz Y. , Milias-Argeitis Andreas
Published: December 2022

Target of Rapamycin Complex 1 (TORC1) and Protein Kinase A (PKA) are two major regulators of cell growth inSaccharomyces cerevisiae, coupling nutrient availability with resource-intensive anabolic processes such as ribosome biogenesis. Even though TORC1 and PKA signaling converge on several shared targets, little is known on how these targets integrate signals from the two pathways. This is the case for Sfp1, a transcriptional activator of hundreds of ribosomal protein and ribosome biogenesis genes. To disentangle the roles of PKA and TORC1 in Sfp1 regulation, we constructed a large collection of Sfp1 (phospho)mutants and studied their intracellular localization and phosphorylation. Besides the already known TORC1 phosphorylation sites, we discovered that Sfp1 contains two PKA sites and a functional Nuclear Export Signal (NES) which is regulated by TORC1 and PKA. We further showed that TORC1 and PKA regulate Sfp1 phosphorylation independently of each other, with loss of activity of either pathway being sufficient to relocalize the protein from the nucleus to the cytoplasm, and the C-terminal zinc fingers being necessary for the responsiveness of Sfp1 to TORC1 and PKA inputs. This work contributes to our understanding of how cells regulate their growth by monitoring the outputs of multiple nutrient-sensing pathways.
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19
Authors: Essex Morgan , Pascual-Leone Belén Millet , Löber Ulrike , Kuhring Mathias , Zhang Bowen , Bruening Ulrike , Fritsche-Guenther Raphaela , Krzanowski Marta , Vernengo Facundo Fiocca , Brumhard Sophia , Röwekamp Ivo , Bielecka Agata Anna , Lesker Till Robin , Wyler Emanuel , Landthaler Markus , Mantei Andrej , Meisel Christian , Caesar Sandra , Thibeault Charlotte , Corman Victor , Marko Lajos , Suttorp Norbert , Strowig Till , Kurth Florian , Sander Leif E. , Li Yang , Kirwan Jennifer A. , Forslund Sofia K. , Opitz Bastian
Published: December 2022

The clinical course of the 2019 coronavirus disease (COVID-19) is variable and to a substantial degree still unpredictable, especially in persons who have neither been vaccinated nor recovered from previous infection. We hypothesized that disease progression and inflammatory responses were associated with alterations in the microbiome and metabolome. To test this, we integrated metagenome, metabolome, cytokine, and transcriptome profiles of longitudinally collected samples from hospitalized COVID-19 patients at the beginning of the pandemic (before vaccines or variants of concern) and non-infected controls, and leveraged detailed clinical information and post-hoc confounder analysis to identify robust within- and cross-omics associations. Severe COVID-19 was directly associated with a depletion of potentially beneficial intestinal microbes mainly belonging to Clostridiales, whereas oropharyngeal microbiota disturbance appeared to be mainly driven by antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine, and reduced levels of various other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Decreased abundance of Clostridiales potentially mediated the observed reduction in 5-hydroxytryptophan levels. Moreover, altered plasma levels of various tryptophan metabolites and lower abundances of Clostridiales explained significant increases in the production of IL-6, IFNγ and/or TNFα. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.

Graphical Abstract
TheKlebsiella pneumoniae teroperon enhances stress tolerance
Authors: Mason Sophia , Vornhagen Jay , Smith Sara N. , Mike Laura A. , Mobley Harry L.T. , Bachman Michael A.
Published: December 2022

Healthcare-acquired infections are a leading cause of disease in patients that are hospitalized or in long-term care facilities.Klebsiella pneumoniae(Kp) is a leading cause of bacteremia, pneumonia, and urinary tract infections in these settings. Previous studies have established that theteroperon, a genetic locus that confers tellurite oxide (K2TeO3) resistance, is associated with infection in colonized patients. Rather than enhancing fitness during infection, theteroperon increases Kp fitness during gut colonization; however, the biologically relevant function of this operon is unknown. First, using a murine model of urinary tract infection, we demonstrate a novel role for theteroperon protein TerC as a bladder fitness factor. To further characterize TerC, we explored a variety of functions, including resistance to metal-induced stress, resistance to ROS-induced stress, and growth on specific sugars, all of which were independent of TerC. Then, using well-defined experimental guidelines, we determined that TerC is necessary for tolerance to ofloxacin, polymyxin B, and cetylpyridinium chloride. We used an ordered transposon library constructed in a Kp strain lacking theteroperon to identify genes required to resist K2TeO3− and polymyxin B-induced stress, which suggested that K2TeO3-induced stress is experienced at the bacterial cell envelope. Finally, we confirmed that K2TeO3disrupts the Kp cell envelope, though these effects are independent ofter. Collectively, the results from these studies indicate a novel role for theteroperon as stress tolerance factor, therefore explaining its role in enhancing fitness in the gut and bladder.
Effect of Potassium Nitrate and Calcium Chloride priming on germination and seedling growth of Honesty (Lunaria annuaL.)
Authors: Bhat Reyaz Ahmad , Khan F U , Bhat Z. A. , Khan F. A. , Wani Javaid Ahmad , Manzar Abu , Nazki I. T , Neelofar  , Altaf Qazi , Masoodi Nasir Hamid
Published: December 2022

Seed priming improves seed performance under environmental conditions. The study was designed to evaluate the effect of different priming treatments on the germination behaviour of Honesty (Lunaria annua L.). The experiment was conducted under a complete randomized design (CRD) with three replications. Seed priming was done with different concentrations of calcium chloride (CaCl2), potassium nitrate (KNO3) and hydro priming. All the treatments except T1(Control) had a significant effect on seedling establishment and seedling vigour, Results show that maximum invigoration was observed in seeds primed at 1% KNO3 while minimum invigoration was observed in T1(Control). It was concluded that the germination percentage could be increased by using lower concentrations of KNO3 and CaCl2.
Within-host viral growth and immune response rates predict FMDV transmission dynamics for African Buffalo
Authors: Macdonald Joshua C. , Gulbudak Hayriye , Beechler Brianna , Gorsich Erin E. , Gubbins Simon , Pérez-Martin Eva , Jolles Anna E.
Published: December 2022

Infectious disease dynamics operate across biological scales: pathogens replicate within hosts but transmit among populations. Functional changes in the pathogen-host interaction thus generate cascading effects across organizational scales. We investigated within-host dynamics and among-host transmission of three strains (SAT-1, 2, 3) of foot-and-mouth disease viruses (FMDVs) in their wildlife host, African buffalo. We combined data on viral dynamics and host immune responses with mathematical models to ask (i) How do viral and immune dynamics vary among strains?; (ii) Which viral and immune parameters determine viral fitness within hosts?; and (iii) How do within-host dynamics relate to virus transmission? Our data reveal contrasting within-host dynamics among viral strains, with SAT-2 eliciting more rapid and effective immune responses than SAT-1 and SAT-3. Within-host viral fitness was overwhelmingly determined by variation among hosts in immune response activation rates but not by variation among individual hosts in viral growth rate. Our analyses investigating across-scale linkages indicate that viral replication rate in the host correlates with transmission rates among buffalo and that adaptive immune activation rate determines the infectious period. These parameters define the virus’s relative basic reproductive number (ℛ0), suggesting that viral invasion potential may be predictable from within-host dynamics.
Y chromosome sequence and epigenomic reconstruction across human populations
Authors: Esteller-Cucala Paula , Palmada-Flores Marc , Kuderna Lukas F. K. , Fontsere Claudia , Serres-Armero Aitor , Dabad Marc , Torralvo María , Faella Armida , Ferrández-Peral Luis , Llovera Laia , Fornas Oscar , Julià Eva , Ramírez Erika , González Irene , Hecht Jochen , Lizano Esther , Juan David , Marquès-Bonet Tomàs
Published: December 2022

Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for 7 major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications amongst the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.
Evolution Inspired Engineering of Megasynthetases
Authors: Bozhüyük Kenan A. J. , Präve Leonard , Kegler Carsten , Kaiser Sebastian , Shi Yan-Ni , Kuttenlochner Wolfgang , Schenk Leonie , Mohiuddin T. M. , Groll Michael , Hochberg Georg K. A. , Bode Helge B.
Published: December 2022

Many clinically used drugs are derived from or inspired by bacterial natural products that often are biosynthesised via non-ribosomal peptide synthetases (NRPS), giant megasynthases that activate and join individual amino acids in an assembly line fashion. Since NRPS are not limited to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would allow the biotechnological generation of complex peptides including linear, cyclic and further modified natural product analogues, e.g. to optimise natural product leads. Here we describe a detailed phylogenetic analysis of several bacterial NRPS that led to the identification of a new recombination breakpoint within the thiolation (T) domain that is important for natural NRPS evolution. From this, an evolution-inspired eXchange Unit between T domains (XUT) approach was developed which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
Multimodal, multiscale connectivity blueprints of the cerebral cortex
Authors: Hansen Justine Y. , Shafiei Golia , Voigt Katharina , Liang Emma X. , Cox Sylvia M. L. , Leyton Marco , Jamadar Sharna D. , Misic Bratislav
Published: December 2022

The brain is composed of disparate neural populations that communicate and interact with one another. Although fiber bundles, similarities in molecular architecture, and synchronized neural activity all represent brain connectivity, a comprehensive study of how all these connectivity modes jointly reflect brain structure and function remains missing. Here we systematically integrate seven multimodal, multiscale brain connectivity profiles derived from gene expression, neurotransmitter receptor density, cellular morphology, glucose metabolism, haemodynamic activity, and electrophysiology. We uncover a compact set of universal organizational principles through which brain geometry and neuroanatomy shape emergent connectivity modes. Connectivity modes also exhibit unique and diverse connection patterns, hub profiles, dominant gradients, and modular organization. Throughout, we observe a consistent primacy of molecular connectivity modes—namely correlated gene expression and receptor similarity—that map well onto multiple phenomena including the rich club and patterns of cortical abnormalities across 13 neurological, psychiatric, and neurodevelopmental disorders. Finally, we fuse all seven connectivity modes into a single multimodal network and show that it maps onto major organizational features of the brain including structural conenctivity, intrinsic functional networks, and cytoarchitectonic classes. Altogether, this work contributes to next-generation connectomics and the integrative study of inter-regional relationships.
Rhoenhancers play unexpectedly minor roles inRhodopsintranscription and rod cell integrity
Authors: Sun Chi , Ruzycki Philip A. , Chen Shiming
Published: December 2022

Enhancers function with a basal promoter to control the transcription of target genes. Enhancer regulatory activity is often studied using reporter-based transgene assays. However, unmatched results have been reported when selected enhancers are silencedin situ. In this study, using genomic deletion analysis in mice, we investigated the roles of two previously identified enhancers and the promoter of theRhogene that codes for the visual pigment rhodopsin. TheRhogene is robustly expressed by rod photoreceptors of the retina, and essential for the subcellular structure and visual function of rod photoreceptors. Mutations inRHOcause severe vision loss in humans. We found that eachRhoregulatory region can independently mediate local epigenomic changes, but only the promoter is absolutely required for establishing activeRhochromatin configuration and transcription and maintaining the cell integrity and function of rod photoreceptors. To our surprise, twoRhoenhancers that enable strong promoter activation in reporter assays are largely dispensable forRhoexpressionin vivo. Only small and age-dependent impact is detectable when both enhancers are deleted. Our results demonstrate context-dependent roles of enhancers and highlight the importance of studying functions ofcis-regulatory regionsin the native genomic context.
Mobile genetic element-encoded putative DNA primases composed of A-family polymerase - SSB pairs
Authors: Rice Phoebe A.
Published: December 2022

1

Mobile genetic elements can encode a wide variety of genes that support their own stability and mobility as well as genes that provide accessory functions to their hosts. Such genes can be adopted from host chromosomes and can be exchanged with other mobile elements. Due to their accessory nature, the evolutionary trajectories of these genes can differ from those of essential host genes. The mobilome therefore provides a rich source of genetic innovation. We previously described a new type of primase encoded byS. aureusSCCmecelements that is composed of an A-family polymerase catalytic domain in complex with a small second protein that confers single-stranded DNA binding. Here we use new structure prediction methods in conjunction with sequence database searches to show that related primases are widespread among putative mobile genetic elements in the Firmicutes. Structure predictions show that the second protein adopts an OB fold (common among single-stranded DNA binding (SSB) proteins) and these predictions were far more powerful than simple sequence comparisons in identifying its homologs. The protein-protein interaction surface varies among these polymerase – SSB complexes and appears to have arisen repeatedly by exploiting partial truncations of the polymerase’s N-terminal accessory domains.
Immortalized bovine satellite cells for cultured meat applications
Authors: Stout Andrew J. , Arnett Miles J. , Chai Kristin M. , Guo Tina , Liao Lishu , Mirliani Addison B. , Rittenberg Miriam L. , Shub Michelle , White Eugene C. , Yuen John S. K. , Zhang Xiaoli , Kaplan David L.
Published: December 2022

For cultured meat to succeed at scale, muscle cells from food-relevant species must be expandedin vitroin a rapid and reliable manner to produce millions of metric tons of biomass annually. Toward this goal, genetically immortalized cells offer substantial benefits over primary cells, including rapid growth, escape from cellular senescence, and consistent starting cell populations for production. Here, we develop genetically immortalized bovine satellite cells (iBSCs) via constitutive expression of bovine Telomerase reverse transcriptase (TERT) and Cyclin-dependent kinase 4 (CDK4). These cells achieve over 120 doublings at the time of publication and maintain their capacity for myogenic differentiation. They therefore offer a valuable tool to the field, enabling further research and development to advance cultured meat.
Determinants of natriuretic, diuretic, and kaliuretic effects of diuretics: Sex and administration time
Authors: Dutta Pritha , Sadria Mehrshad , Layton Anita
Published: December 2022

Sex differences in renal function and blood pressure have been widely described across many species. Blood pressure dips during sleep and peaks in the early morning. Similarly, glomerular filtration rate, filtered electrolyte loads, urine volume, and urinary excretion all exhibit notable diurnal rhythms, which reflect, in part, the regulation of renal transporter proteins by circadian clock genes. That regulation is sexually dimorphic; as such, sex and time-of-day are not two independent regulators of kidney function and blood pressure. The objective of this study is to assess the effect of sex and administration time on the natriuretic and diuretic effects of loop, thiazide, and K+-sparing diuretics, which are common treatment for hypertension. Loop diuretics inhibit NKCC2 on the apical membrane of the thick ascending limb, thiazide diuretics inhibit NCC on the distal convoluted tubule, and K+-sparing diuretics inhibit ENaC on the connecting tubule and collecting duct. We simulate Na+transporter inhibition using our sex- and time-of-day-specific computational models of mouse kidney function. Simulations results highlight significant sex and time-of day differences in drug response. Loop diuretics induce larger natriuretic and diuretic effects during the active phase. The natriuretic and diuretic effects of thiazide diuretics exhibit sex and time-of-day differences, whereas these effects of K+-sparing diuretics exhibit significant time-of-day difference in females only. Kaliuretic effect depends on the type of diuretics and time of administration. The present computational models can be a useful tool in chronotherapy, to tailor drug administration time to match the body’s diurnal rhythms to optimize the drug effect.
A screen for modulation of nucleocapsid protein condensation identifies small molecules with anti-coronavirus activity
Authors: Quek Rui Tong , Hardy Kierra S. , Walker Stephen G. , Nguyen Dan T. , de Almeida Magalhães Taciani , Salic Adrian , Gopalakrishnan Sujatha M. , Silver Pamela A. , Mitchison Timothy J.
Published: December 2022

Biomolecular condensates formed by liquid-liquid phase separation have been implicated in multiple diseases. Modulation of condensate dynamics by small molecules has therapeutic potential, but so far, few condensate modulators have been disclosed. The SARS-CoV-2 nucleocapsid (N) protein forms phase separated condensates that are hypothesized to play critical roles in viral replication, transcription and packaging, suggesting that N condensation modulators might have anti-coronavirus activity across multiple strains and species. Here, we show that N proteins from all seven human coronaviruses (HCoVs) vary in their tendency to undergo phase separation when expressed in human lung epithelial cells. We developed a cell-based high-content screening platform and identified small molecules that both promote and inhibit condensation of SARS-CoV-2 N. Interestingly, these host-targeted small molecules exhibited condensate-modulatory effects across all HCoV Ns. Some have also been reported to exhibit antiviral activity against SARS-CoV-2, HCoV-OC43 and HCoV-229E viral infections in cell culture. Our work reveals that the assembly dynamics of N condensates can be regulated by small molecules with therapeutic potential. Our approach allows for screening based on viral genome sequences alone and might enable rapid paths to drug discovery with value for confronting future pandemics.
Application of the IASP grading system for ‘nociplastic pain’ in chronic pain conditions: A field study
Authors: Schmidt Hannah , Drusko Armin , Renz Malika , Schlömp Lea , Tost Heike , Tesarz Jonas , Schuh-Hofer Sigrid , Meyer-Lindenberg Andreas , Treede Rolf-Detlef
Published: December 2022

The concept ‘nociplastic pain’ has been developed for patients in whom clinical and psychophysical findings suggest a predominant central sensitization type of pain that is not fully explained as nociceptive or neuropathic. Here we tested, how well the recently published grading system differentiates between chronic primary pain or chronic secondary pain conditions. We recruited patients with Fibromyalgia (FMS, 41), Complex Regional Pain Syndrome (CRPS, 11), Osteoarthritis (OA, 21) or Peripheral Nerve Injury (PNI, 8). We used clinical history, pain drawings, Quantitative Sensory Testing (QST) and questionnaires to classify patients’ pains as possibly or probably ‘nociplastic’ in nature.

All FMS and CRPS patients exhibited widespread or regional pain that was not explainable by nociceptive nor neuropathic mechanisms. Widespread pain in 12 OA patients was fully explained as nociceptive and regional pain in 4 PNI patients as neuropathic in all but one in each group. QST provided evidence for hypersensitivity in 9/11 CRPS patients but only 27/41 FMS patients (possible ‘nociplastic pain’). 82% of the CRPS patients but only 54% of FMS patients reported a history of hypersensitivity and mental comorbidities (probable ‘nociplastic pain’). We suggest that clinical examination of hypersensitivity should be done in more than one region and that adding a high tender point count as evidence for hypersensitivity phenomena may be useful. Further we suggest to switch the sequence of steps so that self-reported hypersensitivity and comorbidities come before clinical examination of hypersensitivity; Since the ‘nociplastic pain’ concept calls for brainstem and cortical plasticity we discuss in detail potential measurement strategies.
Research on the influencing factors of the citizen adoption process of China's national integrated online government service platform
Authors: Liu Jiaojiao , Li Weidong , Zou Qi , Liu Shuai , Wang Meng , Zheng Jing
Published: December 2022

Purpose

The Chinese government hopes to achieve the goal of benefiting citizens by building a National Integrated Online Government Service Platform (NIOGSP). However, citizens' low adoption of the platform makes it difficult for the government to achieve its goal. Research on the influencing factors of citizen adoption of NIOGSP can help the government fully understand the concerns and needs of its citizens and take targeted measures to increase citizen adoption.

Design/methodology/approach

First, this research builds a model of the citizen adoption process, including attention, retention and motivation, based on an observational learning model. Next, research variables are determined based on social cognitive theory, literature review and real-world needs. Finally, based on the questionnaire survey and structural equation model, the influencing factors of each stage of the citizen adoption process model are studied and the relationship between the three stages of the model is verified.

Findings

Results show that perceived usefulness (PU) and self-efficacy (SE) positively affect attention. SE positively affects retention, while perceived privacy (PP) negatively affects retention. PU, social influence, PP and anxiety positively affect motivation.

Originality/value

The conclusion of this study can provide reference for governments in various countries to establish and improve online one-stop government. In addition, this study verifies the citizen adoption process model and finds that there is no obvious causal relationship between attention and retention, but both have positive effects on motivation.
Critical factors influencing learning from quality failures in the construction of grid infrastructure
Authors: Zhang Qing-Wen , Liao Pin-Chao , Liang Mingxuan , Chan Albert P.C.
Published: December 2022

Purpose

Quality failures in grid infrastructure construction would cause large-scale collapses in power supply and additional expenditures by reworks and repairs. Learning from quality failures (LFQF) extracts experience from previous quality events and converts them into preventive measures to reduce or eliminate future construction quality issues. This study aims to investigate the influence factors of LFQF in the construction of grid infrastructure.

Design/methodology/approach

The related factors of LFQF, including quality management (QM) practices, quality rectification, and individual learning, were identified by reviewing literature about organizational learning and extracting experience from previous failures. A questionnaire survey was distributed to the grid companies in North, Northeast, Northwest, East, Central, and Southwest China. 381 valid responses collected and analyzed using structural equation modeling (SEM) to test the influence of these factors on LFQF.

Findings

The SEM results support that QM practices positively affect individual learning and LFQF. Quality rectification indirectly impacts LFQF via individual learning, while the results did not support the direct link between quality rectification and LFQF.

Practical implications

The findings strengthen practical insights into extracting experience from poor-quality issues and continuous improvement. The contributory factors of LFQF found in this study benefit the practitioners by taking effective measures to enhance organizational learning capability and improve the long-term construction quality performance in the grid infrastructure industry.

Originality/value

Existing research about the application of LFQF still stays at the explorative and conceptual stage. This study investigates the related factors of LFQF, including QM practices, quality rectification, and individual learning, extending the model development of learning from failures (LFF) in construction QM.
Theoretical framework for strategic productivity in manufacturing: the primary transformation model (PTM)
Authors: Guerreiro Érico Daniel Ricardi , Fidelis Reginaldo , Lima Rafael Henrique Palma
Published: December 2022

Purpose

A quantitative theoretical model is proposed to measure how productivity performance can be affected by strategic decisions related to specific competitive priorities.

Design/methodology/approach

This study proposes the Primary Transformation Model (PTM) and an equation to measure cause-and-effect relationships between productivity and competitive priorities.

Findings

The interdependence between productivity and competitive priorities was studied using the PTM and the proposed model indicates that strategies that improve external performance also impact internal productivity. It was also observed that the compatibility between competitive priorities depends on the initial manufacturing conditions and the implementation method adopted.

Research limitations/implications

The proposed model is theoretical and, as such, is an abstraction of reality and does not consider all possible aspects. It consists of a novel approach that still requires further empirical testing. The PTM provides insights about the trade-offs between productivity and strategic objectives, as well, contributes to the ongoing research on manufacturing strategy and can be further developed in future studies.

Practical implications

The main practical implication is to allow companies to relate their strategic decisions to their productivity performance.

Social implications

This research also contributes to societal issues by enabling firms to better align strategic objectives and operations, which ultimately allows offering products more suited to the needs of customers, thus making better use of the required resources and favoring economic growth.

Originality/value

The model proposed allows objective assessment of actions aiming at operational efficiency and effectiveness, in addition to providing insights into cause-and-effect relationships between productivity and competitive priorities. The model can also be used in empirical investigations on manufacturing strategy.
Sukuk and bond dynamics in relation to exchange rate
Authors: Billah Syed Mabruk , Nguyen Thi Thu Ha , Chowdhury Md Iftekhar Hasan
Published: December 2022

Purpose

This study aims to contribute by expanding the existing literature on Sukuk return and volatility and exploring the implications of the Sukuk-exchange rate interactions.

Design/methodology/approach

This study examines the dynamic interactions of Sukuk with exchange rate in 15 countries, employing the Wavelet approach that considers both time and investment horizons.

Findings

The results reveal significant evolving coherence of Sukuk return and volatility with the underlying exchange rate. The relationship is more potent than what this study witnesses in their counterpart bond market. For Sukuk returns, the coherence is negative, whereas it is positive for volatility. Notably, the coherence is strong in the medium to long term and intensifies during extreme economic episodes, especially during the COVID-19 pandemic. These findings are further validated by comparing firm-level matched data for Sukuk and conventional bond.

Originality/value

To the best of the authors’ knowledge, this is the first study that reports the dynamic relationship of Sukuk return and volatility with the underlying exchange rate in 15 countries. Collectively, this study unites valuable insights for faith-based active Islamic investors and cross-border portfolio managers.
Responding to online complaints in webcare by public organizations: the impact on continuance intention and reputation
Authors: Jacobs Sandra , Liebrecht Christine
Published: December 2022

Purpose

Since public sector organizations provide services to citizens but struggle with poor perceptions of their functioning, it is valuable to examine how their online responses to complaints on social media could impact their reputation. Yet, surprisingly little is known about effects of public organizations' webcare. Therefore, this study assesses the impact of the webcare's tone, response strategy and user's involvement on participants’ continuance intention and perceptions of reputation.

Design/methodology/approach

Two experimental studies (Study 1: N = 424; Study 2: N = 203) with an interval of one week were carried out to assess the effects of singular and repeated exposure to webcare by a Dutch public transport organization on the participants' continuance intention and perceived organizational reputation. Study 1 examined the effects of the webcare's tone (corporate vs conversational human voice (CHV)) and response strategy (accommodative vs defensive); Study 2 contained tone of voice and user's involvement (observer vs complainer). The effects of repeated exposure to the webcare's tone were also examined.

Findings

The results indicate that perceptions of CHV in webcare contribute to webcare as reputation management tool, since it leads to immediate higher reputation scores that also remain stable after repeated exposure. Furthermore, people's continuance intention increased after repeated exposure to webcare responses that were perceived as CHV, thus a natural and engaging communication style, indicating this is an effective strategy for customer care as well. No substantial impact was found for response strategy and user's involvement in the complaint handling.

Originality/value

The novelty of this study is that the authors assess the effects of the webcare's tone combined with response strategy and user's involvement in a public sector context with a sector-specific conceptualization of reputation and continuance intention measured after singular and repeated exposure to webcare.